[Question] Can't get going on Mac M2 Chip

❓ General Questions

I have an Apple M2 Max 32GB.
I've created a conda environment (tried Python3.9 and 3.8) and can't seem to figure out how to get MLC to run without errors.

I tried running a prebuilt model:
git clone https://github.com/mlc-ai/binary-mlc-llm-libs.git dist/prebuilt/lib
git clone https://huggingface.co/mlc-ai/Llama-2-7b-chat-hf-q4f16_1-MLC dist/prebuilt/Llama-2-7b-chat-hf-q4f16_1-MLC

Things I was unsure of from documentation:

these are both in my code directory, rather than in the package directory?
If I use prebuilt models, it asks for config files, so I grabbed them from huggingface

I call it from the demo python file using the commands:
model = "dist/prebuilt/Llama-2-7b-chat-hf-q4f16_1-MLC" model_lib = "dist/prebuilt/lib/Llama-2-7b-chat-hf/Llama-2-7b-chat-hf-q4f16_1-metal.so" engine = MLCEngine(model,model_lib=model_lib)
code % python3 test_mlc.py
[2024-05-10 10:35:07] INFO auto_device.py:88: Not found device: cuda:0
[2024-05-10 10:35:08] INFO auto_device.py:88: Not found device: rocm:0
[2024-05-10 10:35:08] INFO auto_device.py:79: Found device: metal:0
[2024-05-10 10:35:09] INFO auto_device.py:88: Not found device: vulkan:0
[2024-05-10 10:35:10] INFO auto_device.py:88: Not found device: opencl:0
[2024-05-10 10:35:10] INFO auto_device.py:35: Using device: metal:0
[2024-05-10 10:35:10] INFO chat_module.py:379: Using model folder: /Users/xxx/work/xxx/code/dist/prebuilt/Llama-2-7b-chat-hf-q4f16_1-MLC
[2024-05-10 10:35:10] INFO chat_module.py:380: Using mlc chat config: /Users/xxx/work/xxx/code/dist/prebuilt/Llama-2-7b-chat-hf-q4f16_1-MLC/mlc-chat-config.json
[2024-05-10 10:35:10] INFO chat_module.py:529: Using library model: dist/prebuilt/lib/Llama-2-7b-chat-hf/Llama-2-7b-chat-hf-q4f16_1-metal.so
[2024-05-10 10:35:10] INFO engine_base.py:124: The selected engine mode is local. We choose small max batch size and KV cache capacity to use less GPU memory.
[2024-05-10 10:35:10] INFO engine_base.py:149: If you don't have concurrent requests and only use the engine interactively, please select mode "interactive".
[2024-05-10 10:35:10] INFO engine_base.py:154: If you have high concurrent requests and want to maximize the GPU memory utilization, please select mode "server".
[10:35:10] /Users/catalyst/Workspace/mlc-ai-package-self-runner/_work/package/package/mlc-llm/cpp/metadata/model.cc:97: Warning: Failed to parse metadata:
{"model_type": "llama", "quantization": "q4f16_1", "context_window_size": 4096, "prefill_chunk_size": 4096, "sliding_window_size": -1, "attention_sink_size": -1, "tensor_parallel_shards": 1, "params": [{"name": "model.embed_tokens.q_weight", "shape": [32000, 512], "dtype": "uint32", "preprocs": []}, {"name": "model.embed_tokens.q_scale", "shape": [32000, 128], "dtype": "float16", "preprocs": []}, {"name": "model.layers.0.self_attn.qkv_proj.q_weight", "shape": [12288, 512], "dtype": "uint32", "preprocs": []}, {"name": "model.layers.0.self_attn.qkv_proj.q_scale", "shape": [12288, 128], "dtype": "float16", "preprocs": []}, {"name":
...
"model.layers.31.post_attention_layernorm.weight", "shape": [4096], "dtype": "float16", "preprocs": []}, {"name": "model.norm.weight", "shape": [4096], "dtype": "float16", "preprocs": []}, {"name": "lm_head.q_weight", "shape": [32000, 512], "dtype": "uint32", "preprocs": []}, {"name": "lm_head.q_scale", "shape": [32000, 128], "dtype": "float16", "preprocs": []}], "memory_usage": {"_initialize_effect": 0, "decode": 34523648, "prefill":<PHONE_NUMBER>, "softmax_with_temperature": 0}}
libc++abi: terminating due to uncaught exception of type std::exception: std::exception

If I try to run it from the huggingface link with
model = "HF://mlc-ai/Llama-2-7b-chat-hf-q4f16_1-MLC"  engine = MLCEngine(model)
I get a multiprocessing error
Traceback (most recent call last): File "test_mlc.py", line 11, in <module>  engine = MLCEngine(model) File "/Users/xxx/miniforge3/envs/llms/lib/python3.8/site-packages/mlc_llm/serve/engine.py", line 1442, in __init__  super().__init__( File "/Users/xxx/miniforge3/envs/llms/lib/python3.8/site-packages/mlc_llm/serve/engine_base.py", line 442, in __init__  ) = _process_model_args(models, device) File "/Users/xxx/miniforge3/envs/llms/lib/python3.8/site-packages/mlc_llm/serve/engine_base.py", line 115, in _process_model_args  model_args: List[Tuple[str, str]] = [_convert_model_info(model) for model in models] File "/Users/xxx/miniforge3/envs/llms/lib/python3.8/site-packages/mlc_llm/serve/engine_base.py", line 115, in <listcomp>  model_args: List[Tuple[str, str]] = [_convert_model_info(model) for model in models] File "/Users/xxx/miniforge3/envs/llms/lib/python3.8/site-packages/mlc_llm/serve/engine_base.py", line 85, in _convert_model_info  model_path, config_file_path = _get_model_path(model.model) File "/Users/xxx/miniforge3/envs/llms/lib/python3.8/site-packages/mlc_llm/chat_module.py", line 363, in _get_model_path  mlc_dir = download_mlc_weights(model) File "/Users/xxx/miniforge3/envs/llms/lib/python3.8/site-packages/mlc_llm/support/download.py", line 153, in download_mlc_weights  file_url, file_dest = future.result() File "/Users/xxx/miniforge3/envs/llms/lib/python3.8/concurrent/futures/_base.py", line 437, in result  return self.__get_result() File "/Users/xxx/miniforge3/envs/llms/lib/python3.8/concurrent/futures/_base.py", line 389, in __get_result  raise self._exception concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending. /Users/xxx/miniforge3/envs/llms/lib/python3.8/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 3 leaked semaphore objects to clean up at shutdown                         warnings.warn('resource_tracker: There appear to be %d '
If I try the cloned version on my local machine:
ValueError: Traceback (most recent call last):
File "/Users/catalyst/Workspace/mlc-ai-package-self-runner/_work/package/package/tvm/src/runtime/relax_vm/ndarray_cache_support.cc", line 255 ValueError: Error when loading parameters from params_shard_0.bin: [10:44:23] /Users/catalyst/Workspace/mlc-ai-package-self-runner/_work/package/package/tvm/src/runtime/relax_vm/ndarray_cache_support.cc:193: Check failed: this->nbytes == raw_data_buffer->length() (65536000 vs. 133) : ValueError: Encountered an corrupted parameter shard. It means it is not downloaded completely or downloading is interrupted. Please try to download again
I appreciate some of these moves might not make sense due to my architecture and what's coming off huggingface, but I've just been trying anything to get it going.

Any tips appreciated,
Thanks you,
Tam
Environmnent:
This file may be used to create an environment using:
$ conda create --name  --file
platform: osx-arm64
annotated-types=0.6.0=pypi_0
anyio=4.3.0=pypi_0
attrs=23.2.0=pypi_0
bzip2=1.0.8=h93a5062_5
ca-certificates=2024.2.2=hf0a4a13_0
certifi=2024.2.2=pypi_0
charset-normalizer=3.3.2=pypi_0
click=8.1.7=pypi_0
cloudpickle=3.0.0=pypi_0
decorator=5.1.1=pypi_0
distro=1.9.0=pypi_0
dnspython=2.6.1=pypi_0
email-validator=2.1.1=pypi_0
exceptiongroup=1.2.1=pypi_0
fastapi=0.111.0=pypi_0
fastapi-cli=0.0.3=pypi_0
filelock=3.14.0=pypi_0
fsspec=2024.3.1=pypi_0
git-lfs=3.5.1=hce30654_0
h11=0.14.0=pypi_0
httpcore=1.0.5=pypi_0
httptools=0.6.1=pypi_0
httpx=0.27.0=pypi_0
idna=3.7=pypi_0
jinja2=3.1.4=pypi_0
libffi=3.4.2=h3422bc3_5
libsqlite=3.45.3=h091b4b1_0
libzlib=1.2.13=h53f4e23_5
markdown-it-py=3.0.0=pypi_0
markupsafe=2.1.5=pypi_0
mdurl=0.1.2=pypi_0
ml-dtypes=0.2.0=pypi_0
mlc-ai-nightly=0.15.dev315=pypi_0
mlc-llm-nightly=0.1.dev1213=pypi_0
mpmath=1.3.0=pypi_0
ncurses=6.5=hb89a1cb_0
networkx=3.1=pypi_0
numpy=1.24.4=pypi_0
openai=1.28.0=pypi_0
openssl=3.3.0=h0d3ecfb_0
orjson=3.10.3=pypi_0
pip=24.0=pyhd8ed1ab_0
prompt-toolkit=3.0.43=pypi_0
psutil=5.9.8=pypi_0
pydantic=2.7.1=pypi_0
pydantic-core=2.18.2=pypi_0
pygments=2.18.0=pypi_0
python=3.8.19=h2469fbe_0_cpython
python-dotenv=1.0.1=pypi_0
python-multipart=0.0.9=pypi_0
pyyaml=6.0.1=pypi_0
readline=8.2=h92ec313_1
regex=2024.5.10=pypi_0
requests=2.31.0=pypi_0
rich=13.7.1=pypi_0
safetensors=0.4.3=pypi_0
scipy=1.10.1=pypi_0
setuptools=69.5.1=pyhd8ed1ab_0
shellingham=1.5.4=pypi_0
shortuuid=1.0.13=pypi_0
sniffio=1.3.1=pypi_0
starlette=0.37.2=pypi_0
sympy=1.12.1rc1=pypi_0
tiktoken=0.6.0=pypi_0
tk=8.6.13=h5083fa2_1
torch=2.3.0=pypi_0
tornado=6.4=pypi_0
tqdm=4.66.4=pypi_0
typer=0.12.3=pypi_0
typing-extensions=4.11.0=pypi_0
ujson=5.9.0=pypi_0
urllib3=2.2.1=pypi_0
uvicorn=0.29.0=pypi_0
uvloop=0.19.0=pypi_0
watchfiles=0.21.0=pypi_0
wcwidth=0.2.13=pypi_0
websockets=12.0=pypi_0
wheel=0.43.0=pyhd8ed1ab_1
xz=5.2.6=h57fd34a_0

Both works on my m2

mlc_llm chat HF://Llama-2-7b-chat-hf-q4f16_1-MLC
mlc_llm serve HF://mlc-ai/Llama-2-7b-chat-hf-q4f16_1-MLC

Amazing! Thank you! I've check that now and both of those commands work for me.  I've also been able to get the python version to run with the cached versions that were generated through those commands.
model = "/Users/xxx/.cache/mlc_llm/model_weights/mlc-ai/Llama-2-7b-chat-hf-q4f16_1-MLC"
model_lib = "/Users/xxx/.cache/mlc_llm/model_lib/31c3a3541d55119244b74860b99d4176.dylib"
Thanks again!

glad it works


[IOTDB-1262] The test fails to be executed independently

The test fails to be executed independently

solution:

@HTHou hi hannan, could you please reivew this PR?
Thanks


Move Injector to It's own external module

It should call patching modules vs being called within a patching module.

https://github.com/secretsquirrel/the-backdoor-factory#the-backdoor-factory-is-no-longer-maintained-or-supported


Throw an ArgumentError in #api_attachment_to_uploaded if any essential values are absent.

@ArtShein
You can test it (#22) locally by adding gem 'readymade', github: 'dmrAnderson/readymade', branch: 'validation_for_api_attachable' to your Gemfile.
@OrestF
Could you please take a look?

@dmrAnderson
tested it, everything works fine.


Add Web Based Piano Project

I have already added a Web-Dev based Keyboard piano project #222
Merge #222  and assign Hacktoberfest label to me

Done bro
Thanks for your contribution..

I wish to contribute. Kindly assign this to me.


Isabelle development

Added two new html files

Added introduction to index.html as well as links to the two new html files

Added quote to greetings in addRandomGreeting() function in script.js

Additionally added to About Me page

Also consider giving this pull request a more descriptive name which summarizes the commits.


Can I provide custom data and continue training Pythia on this new data?

Can I provide custom data and continue training Pythia on this new data? I have data in a specific domain + language and I would like to use Pythia as the base model and simply continue training it with this additional new data. Is this how this would work or do I need to completely start from scratch ( i.e. traning a Pythia from the ground up with this new data ) ?

Yes you can! You’ll need to either use a pre-final checkpoint or warm up the learning rate again, as the learning rate for the final checkpoint is very small. However you can absolutely finetune Pythia models, and many people have already done so both within EleutherAI and at other orgs.


opjav.com

I believe this domain is an Adult(-related) domain --> that have to be blocked as..
I had to pixelate the screenshot, I don't want anyone to see nudity. I hope it's alright.
Domains
Only add the needed one See also #12

opjav.com

Content sources
(Please see #35)

External sources (reference)

Screenshots
Screenshot required

Logger output
External Info

All Submissions:

[x] Have you checked to ensure there aren't other open Merge Requests (MR) or Issues for the same update/change?
[x] Added a Screenshot for prove of Adult contents

Todo

[ ] Added to Source file?
[ ] Added to the RPZ zone adult.mypdns.cloud (@spirillen)

Super, I'll get these on later, testing the PyFunceble v4 right now, if everything goes right, I'll update the build and test script.
Thanks for your contribution

Super, I'll get these on later, testing the PyFunceble v4 right now, if everything goes right, I'll update the build and test script.
Thanks for your contribution


WebSSH Seeds : 2FA TOTP / HOTP feature

Describe the feature
I often use Google Authenticator to generate my 2FA verification codes and sometimes keys are not on all my devices.
Should WebSSH generate them also?
Then it could help to sync 2FA keys across devices.

WebSSH Seeds?

OTP Libraries

lachlanbell/SwiftOTP
mattrubin/OneTimePassword
gaetanomatonti/Uno
freeotp/freeotp-ios

Stoken

[ ] Ability to save WebSSH database
[ ] Ability to sync seeds from WebSSH to Stoken

Stoken

[ ] Ability to save WebSSH database
[ ] Ability to sync seeds from WebSSH to Stoken

Canceled as macOS 13 as all the features wanted


go get fails with "AnnotatedNode does not implement Node"

go verion: 1.4.2
system: ubuntu 14.04
$ go get github.com/cloudfoundry-incubator/spiff
# github.com/cloudfoundry-incubator/spiff/yaml
gopath/src/github.com/cloudfoundry-incubator/spiff/yaml/node.go:23: cannot use AnnotatedNode literal (type AnnotatedNode) as type Node in return argument:
    AnnotatedNode does not implement Node (wrong type for MarshalYAML method)
        have MarshalYAML() (string, interface {})
        want MarshalYAML() (string, interface {}, error)
gopath/src/github.com/cloudfoundry-incubator/spiff/yaml/parser.go:49: cannot use AnnotatedNode literal (type AnnotatedNode) as type Node in return argument:
    AnnotatedNode does not implement Node (wrong type for MarshalYAML method)
        have MarshalYAML() (string, interface {})
        want MarshalYAML() (string, interface {}, error)
gopath/src/github.com/cloudfoundry-incubator/spiff/yaml/parser.go:63: cannot use AnnotatedNode literal (type AnnotatedNode) as type Node in return argument:
    AnnotatedNode does not implement Node (wrong type for MarshalYAML method)
        have MarshalYAML() (string, interface {})
        want MarshalYAML() (string, interface {}, error)
gopath/src/github.com/cloudfoundry-incubator/spiff/yaml/parser.go:66: cannot use AnnotatedNode literal (type AnnotatedNode) as type Node in return argument:
    AnnotatedNode does not implement Node (wrong type for MarshalYAML method)
        have MarshalYAML() (string, interface {})
        want MarshalYAML() (string, interface {}, error)

Hi @samof76, the spiff repo vendors in its dependencies in Godeps/_workspace using the godeps tool.  One would be to use the godep tool to restore the dependencies from the Godeps folder into your main $GOPATH, but this will overwrite what's already there.  Another alternative would just be to prepend the vendor directory to your $GOPATH while doing things like go get, so e.g. GOPATH=$GOPATH/src/github.com/cloudfoundry-incubator/spiff/Godeps/_workspace:$GOPATH go get github.com/cloudfoundry-incubator/spiff.  You can use something like direnv so you don't need to prefix your $GOPATH every time you work out of the spiff directory.
Are you trying to work on the spiff code or are you just trying to install the spiff binary so you can use it?

For context, this looks like fallout from a breaking change to the Marshaler interface in the candiedyaml library, introduced to resolve https://github.com/cloudfoundry-incubator/candiedyaml/issues/11. It may be simpler to update the spiff types to conform to the new interface.

@amitkgupta I am trying to install Spiff, as part of setting up CF.

Consider using an official release rather than building from source.  Statically linked binaries for Darwin and Linux AMD64 architectures are provided.

Closing this issue, feel free to re-open or create a new issue if you have further questions.

Hello,
As they are no official release for Windows users, how to workaround this issue since it is still present :(
Regards,
Anthony

Hey @AnthonyMullerPlayground
The work around would be to use a Linux VM.  If you are deploying to BOSH-Lite, you can use the BOSH-Lite VM itself.  If you are deploying to a real IaaS, you may wish to set up a jumpbox in your IaaS from which you can do all your manifest generation and even deploying.  In production scenarios where you want even your BOSH director firewalled off from the Internet, it's common practice to have the director port 25555 only accessible from within the firewall, and have your jumpboxes be the only externally accessible thing (via SSH).


Console as logging option

Current logging uses noop, sentry, and rollbar. Provide console logger. Might use zerolog or similar, but make sure the library that's being used has minimal dependency (no dependency would be best).

is it mean changing the Noop etc to Zerolog or adding Zerolog to one of them??

may I work with this feature, I will add zerolog if permitted

@falentio Sure, go ahead


statics: replace rdm png logo with svg

closes https://github.com/inveniosoftware/invenio-app-rdm/issues/167

Tests passing https://travis-ci.org/github/inveniosoftware/invenio-app-rdm/builds/693832599
release needed (release commit included). GitHub is not picking up the travis build..


Problem installing Petar on cluster

Hi, I've been trying to install Petar onto a computing cluster. Other codes have built successfully such as ph4, smalln and Kepler. However, when I tried
pip install --no-cache-dir --no-build-isolation --no-clean amuse-petar -v
in my virtual environment, I get the output:
Using pip 23.3.2 from /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/pip (python 3.11)
Collecting amuse-petar
Downloading amuse-petar-2023.11.0.tar.gz (25 kB)
Running command Preparing metadata (pyproject.toml)
WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
running dist_info
creating /tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info
writing /tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/PKG-INFO
writing dependency_links to /tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/dependency_links.txt
writing requirements to /tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/requires.txt
writing top-level names to /tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/top_level.txt
writing manifest file '/tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/SOURCES.txt'
ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any
reading manifest file '/tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '.pyc' found under directory 'src'
warning: no previously-included files matching '.o' found under directory 'src'
warning: no previously-included files matching '~' found under directory 'src'
warning: no previously-included files matching '.pc' found under directory 'src'
warning: no previously-included files matching 'ccache' found under directory 'src'
warning: no previously-included files matching '.a' found under directory 'src'
writing manifest file '/tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/SOURCES.txt'
creating '/tmp/pip-modern-metadata-ip5_8199/amuse_petar-2023.11.0.dist-info'
In this session you have used the AMUSE modules below.
Please cite any relevant articles:
    "AMUSE (2023.11.0)"
            DOI:10.5281/zenodo.1435860
            ADS:2018araa.book.....P (Portegies Zwart, S. & McMillan, S.L.W., 2018)
            ADS:2013CoPhC.183..456P ** (Portegies Zwart, S. et al., 2013)
            ADS:2013A&A...557A..84P ** (Pelupessy, F. I. et al., 2013)
            ADS:2009NewA...14..369P (Portegies Zwart, S. et al., 2009)

Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: amuse-framework in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from amuse-petar) (2023.11.0)
Requirement already satisfied: setuptools>=41.0.0 in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from amuse-framework->amuse-petar) (65.5.0)
Requirement already satisfied: setuptools-scm in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from amuse-framework->amuse-petar) (8.0.4)
Requirement already satisfied: pip>=19.0.0 in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from amuse-framework->amuse-petar) (23.3.2)
Requirement already satisfied: wheel>=0.32 in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from amuse-framework->amuse-petar) (0.42.0)
Requirement already satisfied: docutils>=0.6 in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from amuse-framework->amuse-petar) (0.20.1)
Requirement already satisfied: numpy>=1.2.2 in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from amuse-framework->amuse-petar) (1.26.2)
Requirement already satisfied: pytest>=4.0 in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from amuse-framework->amuse-petar) (7.4.3)
Requirement already satisfied: h5py>=1.1.0 in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from amuse-framework->amuse-petar) (3.10.0)
Requirement already satisfied: iniconfig in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from pytest>=4.0->amuse-framework->amuse-petar) (2.0.0)
Requirement already satisfied: packaging in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from pytest>=4.0->amuse-framework->amuse-petar) (23.2)
Requirement already satisfied: pluggy<2.0,>=0.12 in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from pytest>=4.0->amuse-framework->amuse-petar) (1.3.0)
Requirement already satisfied: typing-extensions in /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages (from setuptools-scm->amuse-framework->amuse-petar) (4.8.0)
Building wheels for collected packages: amuse-petar
Running command Building wheel for amuse-petar (pyproject.toml)
WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
running bdist_wheel
running build
running build_py
creating build
creating build/lib
creating build/lib/amuse
creating build/lib/amuse/community
creating build/lib/amuse/community/petar
copying src/amuse/community/petar/init.py -> build/lib/amuse/community/petar
copying src/amuse/community/petar/_version.py -> build/lib/amuse/community/petar
copying src/amuse/community/petar/download.py -> build/lib/amuse/community/petar
copying src/amuse/community/petar/interface.py -> build/lib/amuse/community/petar
running build_codes
building libraries and community codes
build, for logging, see 'build.log'
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/codes
creating build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/Makefile -> build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/init.py -> build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/_version.py -> build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/download.py -> build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/interface.cc -> build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/interface.h -> build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/interface.py -> build/temp.linux-x86_64-cpython-311/codes/petar
[18:50:07] building petar
error in call, tail output:
26850K .......... .......... .......... .......... ..........  105M
26900K .......... .......... .......... .......... ..........  118M
26950K .......... .......... .......... .......... ..........  123M
27000K .......... .......... .......... .......... .......... 98.9M
27050K .......... .......... .......... .......... .......... 61.0M
27100K .......... .......... .......... .......... .......... 93.2M
27150K .......... .......... .......... .......... .......... 88.6M
27200K .......... .......... .......... .......... ..........  130M
27250K .......... .......... .......... .......... ..........  118M
27300K .......... .......... .......... .......... ..........  126M
27350K .......... .......... .......... .......... .......... 97.3M
27400K .......... .......... .......... .......... ..........  113M
27450K .......... .......... .......... .......... ..........  131M
27500K .......... .......... .......... .......... .......... 87.5M
27550K .......... .......... .......... .......... ..........  130M
27600K .......... .......... .......... .......... ..........  129M
27650K .......... .......... .......... .......... .......... 98.7M
27700K .......... .......... .......... .......... .......... 41.5M
27750K .......... .......... .......... .......... .......... 43.5M
27800K .......... .......... .......... .......... .......... 5.71M
27850K .......... .......... .......... .......... .......... 4.87M
27900K .......... .......... .......... .......... .......... 6.02M
27950K .......... .......... .......... .......... .......... 5.41M
28000K .......... .......... .......... .......... .......... 5.33M
28050K .......... .......... .......... .......... .......... 4.71M
28100K .......... .......... .......... .......... .......... 56.1M
28150K .......... .......... .......... .......... .......... 5.42M
28200K .......... .......... .......... .......... .......... 6.02M
28250K .......... .......... .......... .......... .......... 5.65M
28300K .......... .......... .......... .......... .......... 4.16M
28350K .......... .......... .......... .......... .......... 8.86M
28400K .......... .......... .......... .......... .......... 44.8M
28450K .......... .......... .......... .......... .......... 5.06M
28500K .......... .......... .......... .......... .......... 5.37M
28550K .......... .......... .......... .......... .......... 5.75M
28600K .......... .......... .......... .......... .......... 5.71M
28650K .......... .......... .......... .......... .......... 3.82M
28700K .......... .......... .......... .......... .......... 57.0M
28750K .......... .......... .......... .......... .......... 4.83M
28800K .......... .......... .......... .......... .......... 6.11M
28850K .......... .......... .......... .......... .......... 5.34M
28900K .......... .......... .......... .......... .......... 4.02M
28950K .......... .......... .......... .......... .......... 8.46M
29000K .......... .......... .......... .......... .......... 74.2M
29050K .......... .......... .......... .......... .......... 4.99M
29100K .......... .......... .......... .......... .......... 4.08M
29150K .......... .......... .......... .......... .......... 6.37M
29200K .......... .......... .......... .......... .......... 6.73M
29250K .......... .......... .......... .......... .......... 5.66M
29300K .......... .......... .......... .......... .......... 5.63M
29350K .......... .......... .......... .......... .......... 65.7M
29400K .......... .......... .......... .......... .......... 4.04M
29450K .......... .......... .......... .......... .......... 6.08M
29500K .......... .......... .......... .......... .......... 6.40M
29550K .......... .......... .......... .......... .......... 5.52M
29600K .......... .......... .......... .......... .......... 5.58M
29650K .......... .......... .......... .......... .......... 50.7M
29700K .......... .......... .......... .......... .......... 6.68M
29750K .......... .......... .......... .......... .......... 3.53M
29800K .......... .......... .......... .......               13.0M=1.5s
2024-01-17 18:50:12 (19.1 MB/s) - ‘55b2bafd316805bad22057cf4ee96217735279bf.tar.gz’ saved [30553099]
downloading version 6ccac364e83ab05e4dad27e6eb6abdf7e5c89bcc from https://github.com/lwang-astro/PeTar/archive/6ccac364e83ab05e4dad27e6eb6abdf7e5c89bcc.tar.gz to 6ccac364e83ab05e4dad27e6eb6abdf7e5c89bcc.tar.gz
downloading finished
unpacking 6ccac364e83ab05e4dad27e6eb6abdf7e5c89bcc.tar.gz
done
downloading version a4ff4b3d076535684313a912ea31985c1431f827 from https://github.com/lwang-astro/SDAR/archive/a4ff4b3d076535684313a912ea31985c1431f827.tar.gz to a4ff4b3d076535684313a912ea31985c1431f827.tar.gz
downloading finished
unpacking a4ff4b3d076535684313a912ea31985c1431f827.tar.gz
done
downloading version 55b2bafd316805bad22057cf4ee96217735279bf from https://github.com/FDPS/FDPS/archive/55b2bafd316805bad22057cf4ee96217735279bf.tar.gz to 55b2bafd316805bad22057cf4ee96217735279bf.tar.gz
downloading finished
unpacking 55b2bafd316805bad22057cf4ee96217735279bf.tar.gz
done
sed 's/@VERSION@/'cat src/PeTar/VERSION'_'cat src/SDAR/VERSION'/g' src/PeTar/src/get_version.hpp.in >src/PeTar/src/get_version.hpp
mpicxx /usr/local/shared/python/3.11.4//include -I src/PeTar/src -I src/SDAR/src -I src/FDPS/src  -fPIC -O2 -Wall -std=c++17  -fopenmp -D PARTICLE_SIMULATOR_THREAD_PARALLEL  -D PARTICLE_SIMULATOR_MPI_PARALLEL -D MPICH_IGNORE_CXX_SEEKC -D SOFT_PERT -D AR_TTL -D AR_SLOWDOWN_TREE -D AR_SLOWDOWN_TIMESCALE -D CLUSTER_VELOCITY -D USE_QUAD -D STELLAR_EVOLUTION -D PROFILE -D HARD_CHECK_ENERGY -D TIDAL_TENSOR_3RD -D INTERFACE_DEBUG_PRINT -D INTERFACE_DEBUG -I/mnt/zfsusers/fthompson/amuse/clonedRepo/amuse/lib/stopcond -c -o interface.o interface.cc
In file included from src/PeTar/src/hard.hpp:17:0,
from src/PeTar/src/petar.hpp:72,
from interface.cc:1:
src/PeTar/src/ar_interaction.hpp: In member function ‘int ARInteraction::modifyAndInterruptIter(AR::InterruptBinary&, AR::BinaryTree&)’:
src/PeTar/src/ar_interaction.hpp:774:19: warning: unused variable ‘drdv’ [-Wunused-variable]
Float drdv = pos_red * vel_red;
^~~~
g++: warning: /usr/local/shared/python/3.11.4//include: linker input file unused because linking not done
mpicxx /usr/local/shared/python/3.11.4//include -I src/PeTar/src -I src/SDAR/src -I src/FDPS/src  -fPIC -O2 -Wall -std=c++17  -fopenmp -D PARTICLE_SIMULATOR_THREAD_PARALLEL  -D PARTICLE_SIMULATOR_MPI_PARALLEL -D MPICH_IGNORE_CXX_SEEKC -D SOFT_PERT -D AR_TTL -D AR_SLOWDOWN_TREE -D AR_SLOWDOWN_TIMESCALE -D CLUSTER_VELOCITY -D USE_QUAD -D STELLAR_EVOLUTION -D PROFILE -D HARD_CHECK_ENERGY -D TIDAL_TENSOR_3RD -D INTERFACE_DEBUG_PRINT -D INTERFACE_DEBUG -I/mnt/zfsusers/fthompson/amuse/clonedRepo/amuse/lib/stopcond   -lm  worker_code.cc interface.o   -o petar_worker -L/mnt/zfsusers/fthompson/amuse/clonedRepo/amuse/lib/stopcond -lstopcondmpi
worker_code.cc:60:13: warning: ‘FALSE_BYTE’ defined but not used [-Wunused-variable]
static bool FALSE_BYTE = 0;
^~~~~~~~~~
worker_code.cc:59:13: warning: ‘TRUE_BYTE’ defined but not used [-Wunused-variable]
static bool TRUE_BYTE = 1;
^~~~~~~~~
worker_code.cc:28:13: warning: ‘NEEDS_MPI’ defined but not used [-Wunused-variable]
static bool NEEDS_MPI = true;
^~~~~~~~~
/usr/bin/ld: cannot find /usr/local/shared/python/3.11.4//include: File format not recognized
collect2: error: ld returned 1 exit status
Makefile:85: recipe for target 'petar_worker' failed
make: *** [petar_worker] Error 1
make: Leaving directory '/tmp/pip-install-i7cyy57g/amuse-petar_c86893928e474b5193cd93452d3f2ca1/build/temp.linux-x86_64-cpython-311/codes/petar'

will copy worker: src/amuse/community/petar
petar
Community codes not built (because of errors/ missing libraries):

petar
================================================================================
0 out of 1 codes built, 0 out of 0 libraries built
Traceback (most recent call last):
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in
main()
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/build_meta.py", line 412, in build_wheel
return self._build_with_temp_dir(['bdist_wheel'], '.whl',
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/build_meta.py", line 397, in _build_with_temp_dir
self.run_setup()
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/build_meta.py", line 484, in run_setup
self).run_setup(setup_script=setup_script)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/build_meta.py", line 335, in run_setup
exec(code, locals())
File "", line 43, in
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/init.py", line 87, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 968, in run_commands
self.run_command(cmd)
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
super().run_command(command)
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 987, in run_command
cmd_obj.run()
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/wheel/bdist_wheel.py", line 368, in run
self.run_command("build")
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
self.distribution.run_command(command)
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
super().run_command(command)
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 987, in run_command
cmd_obj.run()
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 132, in run
self.run_command(cmd_name)
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
self.distribution.run_command(command)
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
super().run_command(command)
File "/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 987, in run_command
cmd_obj.run()
File "/tmp/pip-install-i7cyy57g/amuse-petar_c86893928e474b5193cd93452d3f2ca1/support/setup_codes.py", line 1101, in run
raise Exception("No succesful builds detected. Aborting.")
Exception: No succesful builds detected. Aborting.
error: subprocess-exited-with-error

× Building wheel for amuse-petar (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
full command: /mnt/zfsusers/fthompson/amuse/amuse-env-test/bin/python3 /mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmpq6sstx49
cwd: /tmp/pip-install-i7cyy57g/amuse-petar_c86893928e474b5193cd93452d3f2ca1
Building wheel for amuse-petar (pyproject.toml) ... error
ERROR: Failed building wheel for amuse-petar
Failed to build amuse-petar
ERROR: Could not build wheels for amuse-petar, which is required to install pyproject.toml-based projects
I tried to clone the repository and then:
pip install -e .
make framework
make petar.code
but this also failed with the same message. Here are my config.mk and build.log files:
build.log
config.mk.txt
I'd really appreciate any suggestions.
Best,
Fred

You have to install petar from source,  it is not pip-able, in part due to
the gpu requirements.
good luck,
Simon
On Wed, Jan 17, 2024, 20:01 fredt00 @.***> wrote:

Hi, I've been trying to install Petar onto a computing cluster. Other
codes have built successfully such as ph4, smalln and Kepler. However, when
I tried
pip install --no-cache-dir --no-build-isolation --no-clean amuse-petar -v
in my virtual environment, I get the output:
Using pip 23.3.2 from
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/pip
(python 3.11)
Collecting amuse-petar
Downloading amuse-petar-2023.11.0.tar.gz (25 kB)
Running command Preparing metadata (pyproject.toml)
WARNING setuptools_scm.pyproject_reading toml section missing
'pyproject.toml does not contain a tool.setuptools_scm section'
running dist_info
creating /tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info
writing /tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/PKG-INFO
writing dependency_links to
/tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/dependency_links.txt
writing requirements to
/tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/requires.txt
writing top-level names to
/tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/top_level.txt
writing manifest file
'/tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/SOURCES.txt'
ERROR setuptools_scm._file_finders.git listing git files failed -
pretending there aren't any
reading manifest file
'/tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '
.pyc' found under directory 'src' warning: no previously-included files
matching '.o' found under directory 'src'
warning: no previously-included files matching '
~' found under directory 'src' warning: no previously-included files
matching '.pc' found under directory 'src' warning: no previously-included
files matching 'ccache' found under directory 'src' warning: no
previously-included files matching '.a' found under directory 'src'
writing manifest file
'/tmp/pip-modern-metadata-ip5_8199/amuse_petar.egg-info/SOURCES.txt'
creating
'/tmp/pip-modern-metadata-ip5_8199/amuse_petar-2023.11.0.dist-info'
In this session you have used the AMUSE modules below.
Please cite any relevant articles:
"AMUSE (2023.11.0)"
        DOI:10.5281/zenodo.1435860
        ADS:2018araa.book.....P (Portegies Zwart, S. & McMillan, S.L.W., 2018)
        ADS:2013CoPhC.183..456P ** (Portegies Zwart, S. et al., 2013)
        ADS:2013A&A...557A..84P ** (Pelupessy, F. I. et al., 2013)
        ADS:2009NewA...14..369P (Portegies Zwart, S. et al., 2009)

Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: amuse-framework in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from amuse-petar) (2023.11.0)
Requirement already satisfied: setuptools>=41.0.0 in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from amuse-framework->amuse-petar) (65.5.0)
Requirement already satisfied: setuptools-scm in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from amuse-framework->amuse-petar) (8.0.4)
Requirement already satisfied: pip>=19.0.0 in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from amuse-framework->amuse-petar) (23.3.2)
Requirement already satisfied: wheel>=0.32 in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from amuse-framework->amuse-petar) (0.42.0)
Requirement already satisfied: docutils>=0.6 in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from amuse-framework->amuse-petar) (0.20.1)
Requirement already satisfied: numpy>=1.2.2 in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from amuse-framework->amuse-petar) (1.26.2)
Requirement already satisfied: pytest>=4.0 in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from amuse-framework->amuse-petar) (7.4.3)
Requirement already satisfied: h5py>=1.1.0 in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from amuse-framework->amuse-petar) (3.10.0)
Requirement already satisfied: iniconfig in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from pytest>=4.0->amuse-framework->amuse-petar) (2.0.0)
Requirement already satisfied: packaging in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from pytest>=4.0->amuse-framework->amuse-petar) (23.2)
Requirement already satisfied: pluggy<2.0,>=0.12 in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from pytest>=4.0->amuse-framework->amuse-petar) (1.3.0)
Requirement already satisfied: typing-extensions in
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages
(from setuptools-scm->amuse-framework->amuse-petar) (4.8.0)
Building wheels for collected packages: amuse-petar
Running command Building wheel for amuse-petar (pyproject.toml)
WARNING setuptools_scm.pyproject_reading toml section missing
'pyproject.toml does not contain a tool.setuptools_scm section'
running bdist_wheel
running build
running build_py
creating build
creating build/lib
creating build/lib/amuse
creating build/lib/amuse/community
creating build/lib/amuse/community/petar
copying src/amuse/community/petar/init.py ->
build/lib/amuse/community/petar
copying src/amuse/community/petar/_version.py ->
build/lib/amuse/community/petar
copying src/amuse/community/petar/download.py ->
build/lib/amuse/community/petar
copying src/amuse/community/petar/interface.py ->
build/lib/amuse/community/petar
running build_codes
building libraries and community codes
build, for logging, see 'build.log'
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/codes
creating build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/Makefile ->
build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/init.py ->
build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/_version.py ->
build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/download.py ->
build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/interface.cc ->
build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/interface.h ->
build/temp.linux-x86_64-cpython-311/codes/petar
copying src/amuse/community/petar/interface.py ->
build/temp.linux-x86_64-cpython-311/codes/petar
[18:50:07] building petar
error in call, tail output:
26850K .......... .......... .......... .......... .......... 105M
26900K .......... .......... .......... .......... .......... 118M
26950K .......... .......... .......... .......... .......... 123M
27000K .......... .......... .......... .......... .......... 98.9M
27050K .......... .......... .......... .......... .......... 61.0M
27100K .......... .......... .......... .......... .......... 93.2M
27150K .......... .......... .......... .......... .......... 88.6M
27200K .......... .......... .......... .......... .......... 130M
27250K .......... .......... .......... .......... .......... 118M
27300K .......... .......... .......... .......... .......... 126M
27350K .......... .......... .......... .......... .......... 97.3M
27400K .......... .......... .......... .......... .......... 113M
27450K .......... .......... .......... .......... .......... 131M
27500K .......... .......... .......... .......... .......... 87.5M
27550K .......... .......... .......... .......... .......... 130M
27600K .......... .......... .......... .......... .......... 129M
27650K .......... .......... .......... .......... .......... 98.7M
27700K .......... .......... .......... .......... .......... 41.5M
27750K .......... .......... .......... .......... .......... 43.5M
27800K .......... .......... .......... .......... .......... 5.71M
27850K .......... .......... .......... .......... .......... 4.87M
27900K .......... .......... .......... .......... .......... 6.02M
27950K .......... .......... .......... .......... .......... 5.41M
28000K .......... .......... .......... .......... .......... 5.33M
28050K .......... .......... .......... .......... .......... 4.71M
28100K .......... .......... .......... .......... .......... 56.1M
28150K .......... .......... .......... .......... .......... 5.42M
28200K .......... .......... .......... .......... .......... 6.02M
28250K .......... .......... .......... .......... .......... 5.65M
28300K .......... .......... .......... .......... .......... 4.16M
28350K .......... .......... .......... .......... .......... 8.86M
28400K .......... .......... .......... .......... .......... 44.8M
28450K .......... .......... .......... .......... .......... 5.06M
28500K .......... .......... .......... .......... .......... 5.37M
28550K .......... .......... .......... .......... .......... 5.75M
28600K .......... .......... .......... .......... .......... 5.71M
28650K .......... .......... .......... .......... .......... 3.82M
28700K .......... .......... .......... .......... .......... 57.0M
28750K .......... .......... .......... .......... .......... 4.83M
28800K .......... .......... .......... .......... .......... 6.11M
28850K .......... .......... .......... .......... .......... 5.34M
28900K .......... .......... .......... .......... .......... 4.02M
28950K .......... .......... .......... .......... .......... 8.46M
29000K .......... .......... .......... .......... .......... 74.2M
29050K .......... .......... .......... .......... .......... 4.99M
29100K .......... .......... .......... .......... .......... 4.08M
29150K .......... .......... .......... .......... .......... 6.37M
29200K .......... .......... .......... .......... .......... 6.73M
29250K .......... .......... .......... .......... .......... 5.66M
29300K .......... .......... .......... .......... .......... 5.63M
29350K .......... .......... .......... .......... .......... 65.7M
29400K .......... .......... .......... .......... .......... 4.04M
29450K .......... .......... .......... .......... .......... 6.08M
29500K .......... .......... .......... .......... .......... 6.40M
29550K .......... .......... .......... .......... .......... 5.52M
29600K .......... .......... .......... .......... .......... 5.58M
29650K .......... .......... .......... .......... .......... 50.7M
29700K .......... .......... .......... .......... .......... 6.68M
29750K .......... .......... .......... .......... .......... 3.53M
29800K .......... .......... .......... ....... 13.0M=1.5s
2024-01-17 18:50:12 (19.1 MB/s) -
‘55b2bafd316805bad22057cf4ee96217735279bf.tar.gz’ saved [30553099]
downloading version 6ccac364e83ab05e4dad27e6eb6abdf7e5c89bcc from
https://github.com/lwang-astro/PeTar/archive/6ccac364e83ab05e4dad27e6eb6abdf7e5c89bcc.tar.gz
to 6ccac364e83ab05e4dad27e6eb6abdf7e5c89bcc.tar.gz
downloading finished
unpacking 6ccac364e83ab05e4dad27e6eb6abdf7e5c89bcc.tar.gz
done
downloading version a4ff4b3d076535684313a912ea31985c1431f827 from
https://github.com/lwang-astro/SDAR/archive/a4ff4b3d076535684313a912ea31985c1431f827.tar.gz
to a4ff4b3d076535684313a912ea31985c1431f827.tar.gz
downloading finished
unpacking a4ff4b3d076535684313a912ea31985c1431f827.tar.gz
done
downloading version 55b2bafd316805bad22057cf4ee96217735279bf from
https://github.com/FDPS/FDPS/archive/55b2bafd316805bad22057cf4ee96217735279bf.tar.gz
to 55b2bafd316805bad22057cf4ee96217735279bf.tar.gz
downloading finished
unpacking 55b2bafd316805bad22057cf4ee96217735279bf.tar.gz
done
sed @.*** https://github.com/Version@/'cat src/PeTar/VERSION'_'cat
src/SDAR/VERSION'/g' src/PeTar/src/get_version.hpp.in

src/PeTar/src/get_version.hpp
mpicxx /usr/local/shared/python/3.11.4//include -I src/PeTar/src -I
src/SDAR/src -I src/FDPS/src -fPIC -O2 -Wall -std=c++17 -fopenmp -D
PARTICLE_SIMULATOR_THREAD_PARALLEL -D PARTICLE_SIMULATOR_MPI_PARALLEL -D
MPICH_IGNORE_CXX_SEEKC -D SOFT_PERT -D AR_TTL -D AR_SLOWDOWN_TREE -D
AR_SLOWDOWN_TIMESCALE -D CLUSTER_VELOCITY -D USE_QUAD -D STELLAR_EVOLUTION
-D PROFILE -D HARD_CHECK_ENERGY -D TIDAL_TENSOR_3RD -D
INTERFACE_DEBUG_PRINT -D INTERFACE_DEBUG
-I/mnt/zfsusers/fthompson/amuse/clonedRepo/amuse/lib/stopcond -c -o
interface.o interface.cc
In file included from src/PeTar/src/hard.hpp:17:0,
from src/PeTar/src/petar.hpp:72,
from interface.cc:1:
src/PeTar/src/ar_interaction.hpp: In member function ‘int
ARInteraction::modifyAndInterruptIter(AR::InterruptBinary&,
AR::BinaryTree&)’:
src/PeTar/src/ar_interaction.hpp:774:19: warning: unused variable ‘drdv’
[-Wunused-variable]
Float drdv = pos_red * vel_red;
^~~~
g++: warning: /usr/local/shared/python/3.11.4//include: linker input file
unused because linking not done
mpicxx /usr/local/shared/python/3.11.4//include -I src/PeTar/src -I
src/SDAR/src -I src/FDPS/src -fPIC -O2 -Wall -std=c++17 -fopenmp -D
PARTICLE_SIMULATOR_THREAD_PARALLEL -D PARTICLE_SIMULATOR_MPI_PARALLEL -D
MPICH_IGNORE_CXX_SEEKC -D SOFT_PERT -D AR_TTL -D AR_SLOWDOWN_TREE -D
AR_SLOWDOWN_TIMESCALE -D CLUSTER_VELOCITY -D USE_QUAD -D STELLAR_EVOLUTION
-D PROFILE -D HARD_CHECK_ENERGY -D TIDAL_TENSOR_3RD -D
INTERFACE_DEBUG_PRINT -D INTERFACE_DEBUG
-I/mnt/zfsusers/fthompson/amuse/clonedRepo/amuse/lib/stopcond -lm
worker_code.cc interface.o -o petar_worker
-L/mnt/zfsusers/fthompson/amuse/clonedRepo/amuse/lib/stopcond -lstopcondmpi
worker_code.cc:60:13: warning: ‘FALSE_BYTE’ defined but not used
[-Wunused-variable]
static bool FALSE_BYTE = 0;
^~~~~~~~~~
worker_code.cc:59:13: warning: ‘TRUE_BYTE’ defined but not used
[-Wunused-variable]
static bool TRUE_BYTE = 1;
^~~~~~~~~
worker_code.cc:28:13: warning: ‘NEEDS_MPI’ defined but not used
[-Wunused-variable]
static bool NEEDS_MPI = true;
^~~~~~~~~
/usr/bin/ld: cannot find /usr/local/shared/python/3.11.4//include: File
format not recognized
collect2: error: ld returned 1 exit status
Makefile:85: recipe for target 'petar_worker' failed
make: *** [petar_worker] Error 1
make: Leaving directory
'/tmp/pip-install-i7cyy57g/amuse-petar_c86893928e474b5193cd93452d3f2ca1/build/temp.linux-x86_64-cpython-311/codes/petar'

will copy worker: src/amuse/community/petar
petar
Community codes not built (because of errors/ missing libraries):

petar

================================================================================
0 out of 1 codes built, 0 out of 0 libraries built
Traceback (most recent call last):
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py",
line 353, in
main()
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py",
line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py",
line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/build_meta.py",
line 412, in build_wheel
return self._build_with_temp_dir(['bdist_wheel'], '.whl',
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/build_meta.py",
line 397, in _build_with_temp_dir
self.run_setup()
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/build_meta.py",
line 484, in run_setup
self).run_setup(setup_script=setup_script)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/build_meta.py",
line 335, in run_setup
exec(code, locals())
File "", line 43, in
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/
init.py", line 87, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/core.py",
line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/core.py",
line 201, in run_commands
dist.run_commands()
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/dist.py",
line 968, in run_commands
self.run_command(cmd)
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/dist.py",
line 1217, in run_command
super().run_command(command)
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/dist.py",
line 987, in run_command
cmd_obj.run()
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/wheel/bdist_wheel.py",
line 368, in run
self.run_command("build")
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/cmd.py",
line 319, in run_command
self.distribution.run_command(command)
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/dist.py",
line 1217, in run_command
super().run_command(command)
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/dist.py",
line 987, in run_command
cmd_obj.run()
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/command/build.py",
line 132, in run
self.run_command(cmd_name)
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/cmd.py",
line 319, in run_command
self.distribution.run_command(command)
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/dist.py",
line 1217, in run_command
super().run_command(command)
File
"/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/setuptools/_distutils/dist.py",
line 987, in run_command
cmd_obj.run()
File
"/tmp/pip-install-i7cyy57g/amuse-petar_c86893928e474b5193cd93452d3f2ca1/support/setup_codes.py",
line 1101, in run
raise Exception("No succesful builds detected. Aborting.")
Exception: No succesful builds detected. Aborting.
error: subprocess-exited-with-error
× Building wheel for amuse-petar (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem
with pip.
full command: /mnt/zfsusers/fthompson/amuse/amuse-env-test/bin/python3
/mnt/zfsusers/fthompson/amuse/amuse-env-test/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py
build_wheel /tmp/tmpq6sstx49
cwd: /tmp/pip-install-i7cyy57g/amuse-petar_c86893928e474b5193cd93452d3f2ca1
Building wheel for amuse-petar (pyproject.toml) ... error
ERROR: Failed building wheel for amuse-petar
Failed to build amuse-petar
ERROR: Could not build wheels for amuse-petar, which is required to
install pyproject.toml-based projects
I tried to clone the repository and then:
pip install -e .
make framework
make petar.code
but this also failed with the same message. Here are my config.mk and
build.log files:
build.log https://github.com/amusecode/amuse/files/13967491/build.log
config.mk.txt
https://github.com/amusecode/amuse/files/13967500/config.mk.txt
I'd really appreciate any suggestions.
Best,
Fred
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Hi Simon,
Thanks for the quick reply. I did manage to install amuse-petar via pip on my laptop and it seems to run correctly, so I was hoping this would also be possible on a cluster.
Fred

Installing PeTar via pip is possible - but as Simon said, not with GPU support.
From the error you get it looks to me like there's an error with your Python environment:
/usr/bin/ld: cannot find /usr/local/shared/python/3.11.4//include: File format not recognized
Are you indeed using Python 3.11.4? Have you loaded the right module for this? If so, could you check this directory?

I bet if you did echo ${CXXFLAGS} it would show that /usr/local/shared/python/3.11.4//include. That's not a valid C++ compiler flag, so the compiler rejects it and the build fails.
How did you make Python 3.11 available? If it's through a module then that module is probably broken in that it doesn't set the environment correctly...

I loaded the module python3.11.4 to create the virtual environment. Checking the directory gives:
/usr/local/shared/python/3.11.4/include/python3.11$ ls
abstract.h         datetime.h             frameobject.h         methodobject.h  pycapsule.h    pymacro.h    pytypedefs.h    tupleobject.h
bltinmodule.h      descrobject.h          genericaliasobject.h  modsupport.h    pyconfig.h     pymath.h     rangeobject.h   typeslots.h
boolobject.h       dictobject.h           import.h              moduleobject.h  py_curses.h    pymem.h      setobject.h     unicodeobject.h
bytearrayobject.h  dynamic_annotations.h  internal              object.h        pydtrace.h     pyport.h     sliceobject.h   warnings.h
bytesobject.h      enumobject.h           intrcheck.h           objimpl.h       pyerrors.h     pystate.h    structmember.h  weakrefobject.h
ceval.h            errcode.h              iterobject.h          opcode.h        pyexpat.h      pystrcmp.h   structseq.h
codecs.h           exports.h              listobject.h          osdefs.h        pyframe.h      pystrtod.h   sysmodule.h
compile.h          fileobject.h           longobject.h          osmodule.h      pyhash.h       Python.h     token.h
complexobject.h    fileutils.h            marshal.h             patchlevel.h    pylifecycle.h  pythonrun.h  traceback.h
cpython            floatobject.h          memoryobject.h        pybuffer.h      pymacconfig.h  pythread.h   tracemalloc.h
so it looks like the python directory is correct. When I type echo ${CXXFLAGS} into the terminal nothing is returned.

Yes, echo $INCLUDE does return /usr/local/shared/python/3.11.4//include, but echo $MPICXX also returns nothing.

Ah, that would be the issue then. It seems like the PeTaR Makefile and whatever set that INCLUDE variable disagree on the required syntax. I'm not sure who's right, but unset INCLUDE or export INCLUDE= and then compiling again should fix at least this error.

That solved the problem! Petar now builds and runs successfully. Thanks for the help!

 I'll close this issue now, please open a new one if you run into any other issues.


Fix crash: user can open downloaded video

Description
MA-
When a video is downloaded and then opened, the application crashes. Unfortunately, this behavior was accidentally introduced in PR #803 while adding support for Youtube.
I tested this on the latest version of master as of 10:30pm PST on 17 October, 2016 and manually confirmed on a private server that both downloaded and Youtube videos behave as expected.
How to test this PR
Try downloading a video by navigating to a video unit in My Courses. Then, navigate to My Videos and try to watch that video. The application will crash.
Reviewers
If you've been tagged for review, please "Start a review" with the Github GUI.

[ ] Code review: @saeedbashir
[ ] Code review: @danialzahid94
[ ] Code review: @BenjiLee

Thanks for the pull request, @jaimeohm! I've created OSPR-1515 to keep track of it in JIRA. JIRA is a place for product owners to prioritize feature reviews by the engineering development teams.
Feel free to add as much of the following information to the ticket:

supporting documentation
edx-code email threads
timeline information ("this must be merged by XX date", and why that is)
partner information ("this is a course on edx.org")
any other information that can help Product understand the context for the PR

All technical communication about the code itself will still be done via the GitHub pull request interface. As a reminder, our process documentation is here.
We can't start reviewing your pull request until you've submitted a     signed contributor agreement     or indicated your institutional affiliation.     If you like, you can add yourself to the AUTHORS      file for this repo, though that isn't required.     Please see the CONTRIBUTING     file for more information.

@jaimeohm Thank you for your PR. We appreciate you taking the time to make the contribution.
Please submit a signed contributor agreement to us so we can review this pull request. We realize it's additional work in this case, but you only have to do this once and we're hoping you would make future contributions as well.

@gsong Done! I signed the contributor agreement and sent it to<EMAIL_ADDRESS>

Ah, this makes sense now. It happens when the config setting is NEW_LOGISTRATION_ENABLED: false.

@jaimeohm In the meantime, you might want to review the Travis failures and see if there's anything you need to adjust.

@jaimeohm Don't worry about the tests, they have been flaky lately. I'll let you know if anything actually fails.

Current coverage is 23.24% (diff: 100%)

Merging #826 into master will increase coverage by 0.18%

@@             master       #826   diff @@
==========================================
  Files           677        677
  Lines         56400      56410    +10
  Methods           0          0
  Messages          0          0
  Branches          0          0
==========================================
+ Hits          13006      13114   +108
+ Misses        43394      43296    -98
  Partials          0          0

Powered by Codecov. Last update 141c7b0...daf22b7

@BenjiLee @gsong tests pass!

@jaimeohm Could you provide more specific reproduction steps?

@jaimeohm Could you provide some more information about the crash? I can't reproduce the crash but I am noticing that the list of videos is missing when selecting a course card in My Videos/All Videos.

@jaimeohm This problem is addressed with 851


Grammar and sentence flow in FlatList docs

Modified the getItemLayout section such that it is easier to read through. Even though "a priori" technically a correct term, I feel like changing it will save some people (including me) a Google search.

Thank you!


Get CI Green

#713

@vmx let's see what CI tells us now :)

Some new test fails, but browser tests do run! :)

@vmx can you land the rest?

@diasdavid That one needs https://github.com/ipfs/interface-ipfs-core/pull/227#issuecomment-372696424. Either reverting the commit or fixing the tests.
I currently work on a branch with that one reverted trying to fix the other sporadic failures.

One of the recent merges broke the MFS files tests. Reverting https://github.com/ipfs/interface-ipfs-core/pull/227 isn't enough anymore.


WIP: Starting to sort out pytest with filestore

protip: classes need to start with Test, not test or pytest will not find them!  Also worth noting is that classes cannot have __init__ defined or pytest will skip it too

I think __init__ worked for me, so long as I called super().__init__, unless I'm remembering incorrectly...

From their docs:
pytest implements the following standard test discovery:

If no arguments are specified then collection starts from testpaths (if configured) or the current directory. Alternatively, command line arguments can be used in any combination of directories, file names or node ids.
recurse into directories, unless they match norecursedirs
test_*.py or *_test.py files, imported by their test package name.
Test prefixed test classes (without an init method)
test_ prefixed test functions or methods are test items

@tacaswell Can you review this?  pytest is now running on filestore

Any other comments?


Add partial fill support to Cache Service Interface

Cache and UCE Interface modification

fill mask added in data_mem_pkt to indicate the banks being filled
Data field in data_mem_pkt is changed to fill width from data_width
cache_req_critical signal is added
In-progress registers indicating the info of the only one outstanding missed cacheline are added
Corresponding logic like generating writemask to SRAM based on fill mask and checking hitted bank is filled or not are added

We also want to implement these changes in the LCE (with block_width == fill_width)

In-progress register and relevant logic are removed.
Assertion for fill width != block width is added.
IF modification on LCE are added.

LGTM.

Can you rebase on me_dev?
Has this been tested with bank_width != dword_width.  For example, 2-way 512 bit lines?

LGTM.

Can you rebase on me_dev?
Has this been tested with bank_width != dword_width.  For example, 2-way 512 bit lines?

It is tested using bp_softcore and bp_processor(single core) on 8-way, 4-way, and 2-way with 512 bit lines.

The branch is now rebased on me_dev
LCE now receives set, assoc, block width, fill width parameters when it is instantiated in bp_core.
The lce_fill_width_p is removed and acache_fill_width_p is added.


Diff colors

First of all, thanks for this colorscheme. I think it is one of the best dark themes out there, if not the best. It's all balanced. My coworkers always ask the name of it in a pair session. Please, make the palette more accessible for ports to other text editors. You did a great job here.
IMHO, this colorscheme fails just in one category: the diff colors. It's hard to tell what has changed at a glance.
I don't understand anything about colors, so I don't know what to suggest to help with this. Maybe, some background colors?

First of all, thanks for this colorscheme

Thanks for using it!

About the diff colors, I agree that right now they don't look very good. I didn't put much thought into it. I'll see what other colorschemes are using, hopefully I'll find a useful convention.
I think Neovim will change the diff algorithm in the future, so that might help too.


active editor not always correct...

From time to time the integration tests fail and that's because the active editor isn't the editor that just got opened. That actually a problem not a flawed test... Below a trace I could extract with the following extension snippet

apply this patch to add logging patch.txt
have the extension snippet below, bind the command to a keybindg
execute the command and notice that it breaks after one iteration

      vscode.window.onDidChangeActiveTextEditor(e => {
        console.log('ACTIVE editor -> ' + (e ? e.document.fileName : '<none>'));
    })

    vscode.commands.registerCommand('extension.sayHello', async () => {
        console.log('START')

        const [docA, docB] = await Promise.all([
            vscode.workspace.openTextDocument('/Users/jrieken/Code/_samples/virtual/out/extension.js'),
            vscode.workspace.openTextDocument('/Users/jrieken/Code/_samples/virtual/out/extension.js.map')
        ]);

        let c = 3;
        while (c > 0) {
            console.log('NEW ROUND');
            console.log('want', docA.fileName, c);
            let editorA = await vscode.window.showTextDocument(docA, vscode.ViewColumn.One);
            if (vscode.window.activeTextEditor !== editorA) {
                console.log('editorA BAD', editorA.document.fileName, c);
                break;
            }
            console.log('want', docB.fileName, c);
            let editorB = await vscode.window.showTextDocument(docB, vscode.ViewColumn.Two);
            if (vscode.window.activeTextEditor !== editorB) {
                console.log('editorB BAD', editorB.document.fileName, c);
                break;
            }
            c -= 1;
        }
    });

[Extension Host] NEW ROUND (at /Users/jrieken/Code/_samples/virtual/out/extension.js:49:21)
console.js:100 [Extension Host] want /Users/jrieken/Code/_samples/virtual/out/extension.js 2 (at /Users/jrieken/Code/_samples/virtual/out/extension.js:50:21)
console.js:100 [Extension Host] editorA BAD /Users/jrieken/Code/_samples/virtual/out/extension.js 2 (at /Users/jrieken/Code/_samples/virtual/out/extension.js:53:25)
mainThreadDocumentsAndEditors.js:168     at MainThreadDocumentAndEditorStateComputer._updateState (file:///Users/jrieken/Code/vscode/out/vs/workbench/api/electron-browser/mainThreadDocumentsAndEditors.js:168:25)
    at file:///Users/jrieken/Code/vscode/out/vs/workbench/api/electron-browser/mainThreadDocumentsAndEditors.js:142:113
    at Emitter.fire (file:///Users/jrieken/Code/vscode/out/vs/base/common/event.js:103:38)
console.js:100 [Extension Host] ACTIVE editor -> /Users/jrieken/Code/_samples/virtual/out/extension.js (at vscode.window.onDidChangeActiveTextEditor.e (/Users/jrieken/Code/_samples/virtual/out/extension.js:39:17))

Removing tests should be reverted once this is fixed: https://github.com/Microsoft/vscode/commit/efb435854adaf10f18014fd2df6ff25a85b3eac9

@bpasero @alexandrudima Not sure how this should work. I see that focus isn't called from the workbench when opening a document that is already open. Still, while the editor takes focus there is no event emitted.

There is something fishy going on, I also sometimes see 2 blinking cursors in the editor area when running the sample. I extracted https://github.com/Microsoft/vscode/issues/49330 to look into this and see if the workbench is doing something weird.

verified by running the code above without seeing any BAD


Fallback for bio.tools

Currently bio.tools is down (API and server) ... but all the data from last week is stored here as well https://github.com/research-software-ecosystem/content; I would propose we write a fallback, that pulls the data from there in case bio.tools is down or stays down,
https://github.com/bebatut/galaxy_tool_extractor/blob/ce4b94cd4404f7751fb15101598c4a0bcacd4b8c/bin/extract_galaxy_tools.py#L261-L274

quick fix: https://github.com/bebatut/galaxy_tool_extractor/pull/15, will still work on the fallback


Add support OpenAI GPT-4 Turbo model

Describe the need of your request
OpenAI have released a new version of GPT 4. It is better, faster and cheaper.
Please add support for it
Proposed solution
No response
Additional context
No response

GPT-4 Turbo is available in version 2.2.2.
https://github.com/carlrobertoh/CodeGPT/issues/261

Sorry, I thought I had already updated. thank you very much!
@carlrobertoh


CLJS serialization story for SVG

For CLJ hiccup serializes SVG's as in
#?(:clj
   (defn serialize
     ^String [svg] (str xml-preamble (html {:mode :xml} svg))))

I have tried multiple alternatives for CLJS (hiccups, hipo and sablono for react), which AFAIK each miss an :xml mode.
sablono works properly for the area and line plot example, but fails when used with the bar graph.
In Om the following returns a valid react component based on the line-plot example:
(ns geom-test.geom
  (:require
    [om.core :as om :include-macros true]
    [sablono.core :refer-macros [html]]
    [thi.ng.geom.viz.core :as viz]
    [thi.ng.geom.svg.core :as svg]
    [thi.ng.math.core :as m :refer [PI]]))

(defn test-equation
  [t] (let [x (m/mix (- PI) PI t)] [x (* (Math/cos (* 0.5 x)) (Math/sin (* x x x)))]))

(def viz-spec
  {:x-axis (viz/linear-axis
             {:domain [(- PI) PI] :range [50 580] :major (/ PI 2) :minor (/ PI 4) :pos 250})
   :y-axis (viz/linear-axis
             {:domain     [-1 1] :range [250 20] :major 0.2 :minor 0.1 :pos 50
              :label-dist 15 :label {:text-anchor "end"}})
   :grid   {:attribs {:stroke "#caa"}
            :minor-y true}
   :data   [{:values  (map test-equation (m/norm-range 200))
             :attribs {:fill "none" :stroke "#0af"}
             :layout  viz/svg-line-plot}]})

(defn line-plot [_ owner]
  (om/component
    (html
      [:svg {:width 600 :height 320}
       (viz/svg-plot2d-cartesian viz-spec)])))

I'm more of a reagent kinda person, so no 1st hand experience with sablono / om... But am really suprised that the bar graph fails of all the methods (which only uses rects & lines). Do you get an error of it just doesn't produce a DOM fragment? The svg-plot2d-cartesian just produces hiccup vectors with nothing special. However for React components the issue is that attribs like :fill, :stroke etc. need to be nested under the :style key in the :attribs map. So instead of:
:attribs {:fill "none" :stroke "#0af"}

...you'll need to state these as:
:attribs {:style {:fill "none" :stroke "#0af"}}

(I don't know if that's the same in Om, but I guess so...)
For a non-React based example, check out the SVG physics demo here:
Source: https://github.com/thi-ng/demos/blob/master/geom/src/physics_demos/strands.cljs
Live: http://demo.thi.ng/geom/physics/strands.html
This demo uses the hiccup serializer in the domus lib

The line-plot actually renders perfectly, apparently chrome also accepts tag attributes for properties like fill. I got really excited when it worked. I thought: finally a D3 replacement where I could add event handlers in a data transformation step before passing it to sablono.
The bar graph breaks something in sablono's html macro. The grid renders properly. Everything else ends up outside of the svg tag, rendered in spans as react does with strings:

I think this is really a shortcoming of sablono and other serializers. The bar graph hiccup looks like this below and serializes fine into an SVG DOM using my domus lib or in CLJ w/ hiccup:
[:g
 nil
 ([:g
   {:stroke "#ccc", :stroke-dasharray "1 1"}
   (([:line {:x1 "50.00", :y1 "280.00", :x2 "50.00", :y2 "20.00"}]
     [:line {:x1 "81.18", :y1 "280.00", :x2 "81.18", :y2 "20.00"}]
     ...)
    ([:line {:x1 "50.00", :y1 "267.00", :x2 "580.00", :y2 "267.00"}]
     [:line {:x1 "50.00", :y1 "241.00", :x2 "580.00", :y2 "241.00"}]
     ...))]
  ([:g
    {:stroke "#0af", :stroke-width "19px"}
    (([:line {:x1 "81.18", :y1 "195.10", :x2 "81.18", :y2 "280.00"}]
      ...))])
  [:g
   {:stroke "black"}
   (([:line {:x1 "50.00", :y1 "280.00", :x2 "50.00", :y2 "290.00"}]
     ...)
    ()
    [:g
     {:stroke "none",
      :fill "black",
      :font-family "Arial, sans-serif",
      :font-size 10,
      :text-anchor "middle"}
     (([:text {:x "50.00", :y "300.00"} 1999]
       ...))]
    [:line {:x1 "50.00", :y1 "280.00", :x2 "580.00", :y2 "280.00"}])]
  [:g
   {:stroke "black"}
   (([:line {:x1 "50.00", :y1 "280.00", :x2 "40.00", :y2 "280.00"}]
     ...)
    ([:line {:x1 "50.00", :y1 "267.00", :x2 "45.00", :y2 "267.00"}]
     ...)
    [:g
     {:stroke "none",
      :fill "black",
      :font-family "Arial, sans-serif",
      :font-size 10,
      :text-anchor "end"}
     (([:text {:x "35.00", :y "280.00"} "0.00"]
       ...))]
    [:line {:x1 "50.00", :y1 "280.00", :x2 "50.00", :y2 "20.00"}])])]

I guess, it's the nested seqs which cause the serialization "hiccup" (pun intended! :) Will have to check if I can switch to mapcat somewhere.

thanks @postspectacular I'm a huge fan of the geom toolkit. Looking forward to use it more & more in the future!

Hi @den1k - just checked in 2 pieces of functionality which now cause no more warnings when using the viz module with Reagent (still not tried with sablono or any other Om related libs).
Seqs of elements in SVG groups now have one level less of nesting and you'll need to insert a call to inject-element-attribs (in the thi.ng.geom.svg.adapter ns). This fn will generate unique IDs for each element in the SVG hiccup structure.
The below is a complete reagent component for reference:
(defn visualization
  "Takes a geom.viz visualization spec map and generates a SVG component.
  The call to inject-element-attribs ensures that all SVG elements have
  an unique :key attribute, required for React.js."
  [spec]
  (->> spec
       (viz/svg-plot2d-cartesian)
       (svgadapt/inject-element-attribs svgadapt/key-attrib-injector)
       (svg/svg {:width 600 :height 600})))

It'd be great if you could test this with any of the other libs.
Latest release version is: [thi.ng/geom "0.0.908"]

Thanks @postspectacular for adding keys! The bar chart now renders properly. I checked the line chart which has extra numbers in it's last svg group node.
It appears that the group should contain svg text nodes but instead it has plain numbers which react renders as spans.

I don't know what you're seeing with that above linked demo, but I get the same (good & expected) results in Chrome (46.0.2490.86), FF(42.0) and even Safari 6.0.5 (8536.30.1):

Screenshots from Chrome, but worrying that you seem to be seeing something else... I also don't see any React warnings in the console for any of these viz methods. What browser & version you're testing with?
If you want to try, the source for that demo is in this repo: https://github.com/thi-ng/ws-ldn-1

Is there a way to provide a simple example of a working Reagent-based SVG for working with, say, shapes?
I'm trying the following and it's not working out:
(defn svg-component [width body]
  [:div
   [(->> body
         (svgadapt/inject-element-attribs svgadapt/key-attrib-injector)
         (svg/svg {:width width :height width}))]])

(defn simple []
  (svg-component 300 (svg/group {:stroke "blue" :fill "none"} (c/circle 20))))

(defn ^:export on-js-reload []
  (r/render [simple]
            (js/document.getElementById "app")))

I get Error rendering component (in things.core.simple and Uncaught Error: Invalid arity: 1 with pretty useless stack traces.

Hi @Polyrhythm - there're two things wrong with your example:

In svg-component - you don't want to wrap the child of the inner form in a vector, since then your structure would look like this: [:div [[:svg ... ]]] and this causes part of the trouble
The other issue is that you forgot to call svgadapt/all-as-svg before injecting the :key attribs

So corrected, this works without a hitch:
(defn svg-component [width body]
  [:div
   (->> body
        (svgadapt/all-as-svg)
        (svgadapt/inject-element-attribs svgadapt/key-attrib-injector)
        (svg/svg {:width width :height width}))])

(defn simple []
  (svg-component 300 (svg/group {:stroke "blue" :fill "none"} (c/circle 20))))

(defn ^:export main []
  (reagent/render
   [simple]
   (js/document.getElementById "app")))

@postspectacular thank you for the quick and thorough reply. Now I can get started learning this awesome set of tools. 👍


No sound

I am  using a RPI Zero with python3. When attempting to "Generating DTMF audio from a dial string" everything seems to work well as I get no errors. Yet I am not getting the audio of the generated tones. No doubt I am not doing something right. I am as new as you can get with python.

The generate() function returns the audio sample data that, when played back, results in the DTMF tone sequence you requested.  You will need to write additional code to do something with that audio data, such as play it back via an audio device on the machine, save it to an audio file for later playback, etc.

Thank you for your response. I appreciate your effort to write and post the code. Unfortunately, I don't have the expertise to use the data in a viable method.
Several years ago I embarked on an adventure to create a cellular payphone. The project involved the below:

an old payphone.
Arduino 2560 Mega.
LTE1690 IC to generated Touchtone.
LMC6484IN to generate dialtone.
MT8870 to decode touch tone.
SIM900 to make cell calls
4 relay module.

The Arduino was used to interface between the various modules. Collecting coin values before a call was allowed. Collecting and sending dialed digits to the sim900. Refunding or keeping money if the call was not or was successful, etc..  Happily the project was a success and has worked well... Unfortunately when 2G was shutdown in the US the SIM900 no longer works for making calls.
I've have ordered a SIM7600A-H that works with 4G. There are references to it being used on the PI. I was hoping by using the Pi I could eliminate the use of the IC's and DTMF decoder.
I guess I will just stick with what I have and try to get the SIM7600 working on the  Arduino. Thanks again!

This library also has the ability to decode DTMF from an audio buffer; you just have to write the code to receive the audio buffer from your audio input device and pass it to the detect() function.
At any rate, sounds like an interesting project.  I wish you the best of luck!


Can anyone help on this issue?

solved this issue npm install --save react-addons-shallow-compare

react-addons-shallow-compare is a peerDep. @satya164 should it be dep?

@chirag04 I prefer it to be a peerDep so that the version of react and react-addons-shallow-compare stay in sync. I should document it.