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openforcefield / openff-benchmark

Comparison benchmarks between public force fields and Open Force Field Initiative force fields
MIT License
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Deployment procedure: conda create env fails #41

Open foxth opened 3 years ago

foxth commented 3 years ago

Hi I just tried to set up the environment, but after issueing the commands conda activate (base) bibcinews92001 [foxt]% conda env create openforcefield/openff-benchmark-optimization

I get the following error:

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/connectionpool.py", line 696, in urlopen
    self._prepare_proxy(conn)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/connectionpool.py", line 964, in _prepare_proxy
    conn.connect()
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/connection.py", line 421, in connect
    tls_in_tls=tls_in_tls,
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/util/ssl_.py", line 429, in ssl_wrap_socket
    sock, context, tls_in_tls, server_hostname=server_hostname
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/util/ssl_.py", line 472, in _ssl_wrap_socket_impl
    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
  File "/apps/test/foxt/anaconda3/lib/python3.7/ssl.py", line 423, in wrap_socket
    session=session
  File "/apps/test/foxt/anaconda3/lib/python3.7/ssl.py", line 870, in _create
    self.do_handshake()
  File "/apps/test/foxt/anaconda3/lib/python3.7/ssl.py", line 1139, in do_handshake
    self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1091)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/requests/adapters.py", line 449, in send
    timeout=timeout
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/connectionpool.py", line 756, in urlopen
    method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/util/retry.py", line 573, in increment
    raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='api.anaconda.org', port=443): Max retries exceeded with url: /package/openforcefield/openff-benchmark-optimization (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1091)')))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 87, in execute
    spec = specs.detect(name=name, filename=filename, directory=os.getcwd())
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/specs/__init__.py", line 43, in detect
    if spec.can_handle():
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/specs/binstar.py", line 45, in can_handle
    result = self._can_handle()
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/specs/binstar.py", line 60, in _can_handle
    return self.package is not None and self.valid_package()
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/specs/binstar.py", line 114, in package
    self._package = self.binstar.package(self.username, self.packagename)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/binstar_client/__init__.py", line 301, in package
    res = self.session.get(url)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/requests/sessions.py", line 555, in get
    return self.request('GET', url, **kwargs)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/requests/sessions.py", line 542, in request
    resp = self.send(prep, **send_kwargs)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/requests/sessions.py", line 655, in send
    r = adapter.send(request, **kwargs)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/requests/adapters.py", line 514, in send
    raise SSLError(e, request=request)
requests.exceptions.SSLError: HTTPSConnectionPool(host='api.anaconda.org', port=443): Max retries exceeded with url: /package/openforcefield/openff-benchmark-optimization (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1091)')))

$ /apps/test/foxt/anaconda3/bin/conda-env create openforcefield/openff-benchmark-optimization

environment variables: CIO_TEST= CLASSPATH=/apps/prod/COMPCHEM/chemaxon/MarvinBeans/lib/MarvinBeans.jar CONDA_AUTO_UPDATE_CONDA=false CONDA_DEFAULT_ENV=base CONDA_EXE=/apps/test/foxt/anaconda3/bin/conda CONDA_PREFIX=/apps/test/foxt/anaconda3 CONDA_PROMPT_MODIFIER=(base) CONDA_PYTHON_EXE=/apps/test/foxt/anaconda3/bin/python CONDA_ROOT=/apps/test/foxt/anaconda3 CONDA_SHLVL=1 CURL_CA_BUNDLE= DRMAA_LIBRARY_PATH=/opt/sge/lib//libdrmaa.so FTP_PROXY= HTTPS_PROXY= HTTP_PROXY= LD_LIBRARY_PATH=/apps/prod/amber/amber18-18_sl7/lib:/usr/local/cuda/lib64:/apps/prod/a mber/amber18-18_sl7/lib:/apps/prod/COMPCHEM/openeye/openeye_2018/java/ libs/Linux-x64/:/apps/prod/COMPCHEM/gaussian/g09/g09/bsd:/apps/prod/CO MPCHEM/gaussian/g09/g09/local:/apps/prod/COMPCHEM/gaussian/g09/g09/ext ras:/apps/prod/COMPCHEM/gaussian/g09/g09::/opt/slurm/prod/lib64:/opt/s lurm/prod/lib64:/apps/prod/COMPCHEM/gaussian/g09/gv/lib LD_RUN_PATH=:/opt/slurm/prod/lib64 MANPATH=/opt/sge/man:/apps/prod/COMPCHEM/gaussian/g09/g09/bsd:/opt/sge/man:/us r/share/lmod/lmod/share/man:/opt/sge/man::/opt/slurm/prod/share/man:/o pt/slurm/prod/share/man:/apps/prod/COMPCHEM/cresset/blaze/current/xed/ man MODULEPATH=/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lm od/lmod/modulefiles/Core NO_PROXY= PATH=/apps/test/foxt/anaconda3/bin:/apps/test/foxt/anaconda3/bin:/apps/test /foxt/anaconda3/condabin:/apps/test/foxt/anaconda3/bin:/apps/test/foxt /anaconda3/bin:/apps/test/foxt/anaconda3/bin:/apps/test/foxt/anaconda3 /bin:/apps/prod/amber/amber18-18_sl7/bin:/opt/slurm/prod/bin:/apps/pro d/amber/amber18-18_sl7/bin:/apps/test/COMPCHEM/DivConDiscoverySuite/Di vConDiscoverySuite/bin:/apps/prod/ccg/moe/bin:/home/foxt/AMBER/ti_scri pts:/home/foxt/bin:/apps/test/foxt/anaconda3/bin:/home/foxt/bin:/apps/ prod/amber/amber18-18_sl7/bin:/apps/prod/COMPCHEM/compchem/vim/current /bin:/apps/prod/COMPCHEM/compchem/vim/bin:/opt/sge/bin:/opt/sge/bin/lx -amd64:/apps/prod/COMPCHEM/knime/bin:/apps/prod/COMPCHEM/schrodinger/c urrent:/apps/prod/COMPCHEM/ccdc/cambridge_2020.0.1/Discovery_2020/bin: /apps/prod/COMPCHEM/ccdc/cambridge_2020.0.1/CSD_2020/bin:/apps/prod/CO MPCHEM/alvaDesc/bin:/opt/sge/bin:/opt/sge/bin/lx- amd64:/usr/lib64/qt-3.3/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/lo cal/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/slurm/prod/bin:/o pt/singularity/bin:/opt/slurm/prod/bin:/opt/singularity/bin:/apps/prod /COMPCHEM/compchem/bin:/apps/prod/COMPCHEM/gaussian/g09/g09/bsd:/apps/ prod/COMPCHEM/gaussian/g09/g09/local:/apps/prod/COMPCHEM/gaussian/g09/ g09/extras:/apps/prod/COMPCHEM/gaussian/g09/g09:/home/foxt/bin/perlscr ipts:/home/foxt/AMBER/ti_scripts PYTHONPATH=/apps/prod/amber/amber18-18_sl7/lib/python2.7/site- packages:/apps/prod/amber/amber18-18_sl7/lib/python2.7/site-packages QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins RASMOLPATH=/apps/prod/COMPCHEM/cresset/blaze/current/xed/xedman REQUESTS_CA_BUNDLE= R_PATH=/apps/prod/COMPCHEM/R/R-current SSL_CERT_FILE= ftp_proxy= http_proxy= https_proxy= no_proxy=

 active environment : base
active env location : /apps/test/foxt/anaconda3
        shell level : 1
   user config file : /home/foxt/.condarc

populated config files : /home/foxt/.condarc conda version : 4.9.2 conda-build version : 3.21.4 python version : 3.7.9.final.0 virtual packages : cuda=10.0=0 glibc=2.17=0 unix=0=0 archspec=1=x86_64 base environment : /apps/test/foxt/anaconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/omnia/linux-64 https://conda.anaconda.org/omnia/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /apps/test/foxt/anaconda3/pkgs /home/foxt/.conda/pkgs envs directories : /apps/test/foxt/anaconda3/envs /home/foxt/.conda/envs platform : linux-64 user-agent : conda/4.9.2 requests/2.25.1 CPython/3.7.9 Linux/3.10.0-514.6.1.el7.x86_64 rhel/7.4 glibc/2.17 UID:GID : 1189:3220 netrc file : None offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve future releases of conda. Would you like conda to send this report to the core maintainers?

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/connectionpool.py", line 696, in urlopen
    self._prepare_proxy(conn)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/connectionpool.py", line 964, in _prepare_proxy
    conn.connect()
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/connection.py", line 421, in connect
    tls_in_tls=tls_in_tls,
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/util/ssl_.py", line 429, in ssl_wrap_socket
    sock, context, tls_in_tls, server_hostname=server_hostname
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/util/ssl_.py", line 472, in _ssl_wrap_socket_impl
    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
  File "/apps/test/foxt/anaconda3/lib/python3.7/ssl.py", line 423, in wrap_socket
    session=session
  File "/apps/test/foxt/anaconda3/lib/python3.7/ssl.py", line 870, in _create
    self.do_handshake()
  File "/apps/test/foxt/anaconda3/lib/python3.7/ssl.py", line 1139, in do_handshake
    self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1091)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/requests/adapters.py", line 449, in send
    timeout=timeout
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/connectionpool.py", line 756, in urlopen
    method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/urllib3/util/retry.py", line 573, in increment
    raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='api.anaconda.org', port=443): Max retries exceeded with url: /package/openforcefield/openff-benchmark-optimization (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1091)')))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 87, in execute
    spec = specs.detect(name=name, filename=filename, directory=os.getcwd())
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/specs/__init__.py", line 43, in detect
    if spec.can_handle():
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/specs/binstar.py", line 45, in can_handle
    result = self._can_handle()
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/specs/binstar.py", line 60, in _can_handle
    return self.package is not None and self.valid_package()
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/conda_env/specs/binstar.py", line 114, in package
    self._package = self.binstar.package(self.username, self.packagename)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/binstar_client/__init__.py", line 301, in package
    res = self.session.get(url)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/requests/sessions.py", line 555, in get
    return self.request('GET', url, **kwargs)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/requests/sessions.py", line 542, in request
    resp = self.send(prep, **send_kwargs)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/requests/sessions.py", line 655, in send
    r = adapter.send(request, **kwargs)
  File "/apps/test/foxt/anaconda3/lib/python3.7/site-packages/requests/adapters.py", line 514, in send
    raise SSLError(e, request=request)
requests.exceptions.SSLError: HTTPSConnectionPool(host='api.anaconda.org', port=443): Max retries exceeded with url: /package/openforcefield/openff-benchmark-optimization (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1091)')))

$ /apps/test/foxt/anaconda3/bin/conda-env create openforcefield/openff-benchmark-optimization

environment variables: CIO_TEST= CLASSPATH=/apps/prod/COMPCHEM/chemaxon/MarvinBeans/lib/MarvinBeans.jar CONDA_AUTO_UPDATE_CONDA=false CONDA_DEFAULT_ENV=base CONDA_EXE=/apps/test/foxt/anaconda3/bin/conda CONDA_PREFIX=/apps/test/foxt/anaconda3 CONDA_PROMPT_MODIFIER=(base) CONDA_PYTHON_EXE=/apps/test/foxt/anaconda3/bin/python CONDA_ROOT=/apps/test/foxt/anaconda3 CONDA_SHLVL=1 CURL_CA_BUNDLE= DRMAA_LIBRARY_PATH=/opt/sge/lib//libdrmaa.so FTP_PROXY= HTTPS_PROXY= HTTP_PROXY= LD_LIBRARY_PATH=/apps/prod/amber/amber18-18_sl7/lib:/usr/local/cuda/lib64:/apps/prod/a mber/amber18-18_sl7/lib:/apps/prod/COMPCHEM/openeye/openeye_2018/java/ libs/Linux-x64/:/apps/prod/COMPCHEM/gaussian/g09/g09/bsd:/apps/prod/CO MPCHEM/gaussian/g09/g09/local:/apps/prod/COMPCHEM/gaussian/g09/g09/ext ras:/apps/prod/COMPCHEM/gaussian/g09/g09::/opt/slurm/prod/lib64:/opt/s lurm/prod/lib64:/apps/prod/COMPCHEM/gaussian/g09/gv/lib LD_RUN_PATH=:/opt/slurm/prod/lib64 MANPATH=/opt/sge/man:/apps/prod/COMPCHEM/gaussian/g09/g09/bsd:/opt/sge/man:/us r/share/lmod/lmod/share/man:/opt/sge/man::/opt/slurm/prod/share/man:/o pt/slurm/prod/share/man:/apps/prod/COMPCHEM/cresset/blaze/current/xed/ man MODULEPATH=/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lm od/lmod/modulefiles/Core NO_PROXY= PATH=/apps/test/foxt/anaconda3/bin:/apps/test/foxt/anaconda3/bin:/apps/test /foxt/anaconda3/condabin:/apps/test/foxt/anaconda3/bin:/apps/test/foxt /anaconda3/bin:/apps/test/foxt/anaconda3/bin:/apps/test/foxt/anaconda3 /bin:/apps/prod/amber/amber18-18_sl7/bin:/opt/slurm/prod/bin:/apps/pro d/amber/amber18-18_sl7/bin:/apps/test/COMPCHEM/DivConDiscoverySuite/Di vConDiscoverySuite/bin:/apps/prod/ccg/moe/bin:/home/foxt/AMBER/ti_scri pts:/home/foxt/bin:/apps/test/foxt/anaconda3/bin:/home/foxt/bin:/apps/ prod/amber/amber18-18_sl7/bin:/apps/prod/COMPCHEM/compchem/vim/current /bin:/apps/prod/COMPCHEM/compchem/vim/bin:/opt/sge/bin:/opt/sge/bin/lx -amd64:/apps/prod/COMPCHEM/knime/bin:/apps/prod/COMPCHEM/schrodinger/c urrent:/apps/prod/COMPCHEM/ccdc/cambridge_2020.0.1/Discovery_2020/bin: /apps/prod/COMPCHEM/ccdc/cambridge_2020.0.1/CSD_2020/bin:/apps/prod/CO MPCHEM/alvaDesc/bin:/opt/sge/bin:/opt/sge/bin/lx- amd64:/usr/lib64/qt-3.3/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/lo cal/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/slurm/prod/bin:/o pt/singularity/bin:/opt/slurm/prod/bin:/opt/singularity/bin:/apps/prod /COMPCHEM/compchem/bin:/apps/prod/COMPCHEM/gaussian/g09/g09/bsd:/apps/ prod/COMPCHEM/gaussian/g09/g09/local:/apps/prod/COMPCHEM/gaussian/g09/ g09/extras:/apps/prod/COMPCHEM/gaussian/g09/g09:/home/foxt/bin/perlscr ipts:/home/foxt/AMBER/ti_scripts PYTHONPATH=/apps/prod/amber/amber18-18_sl7/lib/python2.7/site- packages:/apps/prod/amber/amber18-18_sl7/lib/python2.7/site-packages QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins RASMOLPATH=/apps/prod/COMPCHEM/cresset/blaze/current/xed/xedman REQUESTS_CA_BUNDLE= R_PATH=/apps/prod/COMPCHEM/R/R-current SSL_CERT_FILE= ftp_proxy= http_proxy= https_proxy= no_proxy=

 active environment : base
active env location : /apps/test/foxt/anaconda3
        shell level : 1
   user config file : /home/foxt/.condarc

populated config files : /home/foxt/.condarc conda version : 4.9.2 conda-build version : 3.21.4 python version : 3.7.9.final.0 virtual packages : cuda=10.0=0 glibc=2.17=0 unix=0=0 archspec=1=x86_64 base environment : /apps/test/foxt/anaconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/omnia/linux-64 https://conda.anaconda.org/omnia/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /apps/test/foxt/anaconda3/pkgs /home/foxt/.conda/pkgs envs directories : /apps/test/foxt/anaconda3/envs /home/foxt/.conda/envs platform : linux-64 user-agent : conda/4.9.2 requests/2.25.1 CPython/3.7.9 Linux/3.10.0-514.6.1.el7.x86_64 rhel/7.4 glibc/2.17 UID:GID : 1189:3220 netrc file : None offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve future releases of conda. Would you like conda to send this report to the core maintainers?

I have tried conda config --set ssl_verify false

but this didnt change things.

I checked and I can access the outside world with conda and e.g. update packages...

Any idea?

Best, Th.

j-wags commented 3 years ago

Thanks for the detailed report. I'm unable to reproduce this. My hypotheses at this time are:

ircraig commented 3 years ago

I get the same error. I tried running conda update --all but it didn't make a difference. Is there anything else I should try?

foxth commented 3 years ago

Today it worked. First did a update --all, then conda env create. Then the installation ran through and I can activate the environment.

j-wags commented 3 years ago

@ircraig As a fall-back option, you could try downloading the single-file installer from the Downloads/Assets section of the most recent release on the openff-benchmark github repository (it's the 1.1GB file beginning with ubuntu...). This is linux-only, and contains static copies of all the dependencies so installation doesn't require an internet connection after the initial download. Instructions for installing from that file are here

ircraig commented 3 years ago

OK, thanks. I'll give the single-file installer a try.

foxth commented 3 years ago

Hi Jeff,

 

just want to report that I successfully ran 10 test compounds through the pipeline using option C. Very swift, great work at your end!! How final is the report compare-forcefield part? Here I got a lot of warnings, but the csvfiles were produced.

 

What I do get: in all FF csvfiles I have one conformation (always the same) where the tfd is missing. What is the meaning of this? The compound in itself looks harmless CC(N)C(=O)OC, and the json files look normal, the sdfile has a initial and final energy tag. I guess I can send you the files if this helps...

 

Best,

Th.

   

Gesendet: Montag, 25. Januar 2021 um 19:35 Uhr Von: "Jeff Wagner" notifications@github.com An: "openforcefield/openff-benchmark" openff-benchmark@noreply.github.com Cc: "foxth" Thomas.fox@gmx.net, "Author" author@noreply.github.com Betreff: Re: [openforcefield/openff-benchmark] Deployment procedure: conda create env fails (#41)

 

Thanks for the detailed report. I'm unable to reproduce this. My hypotheses at this time are:

Maybe it was an intermittent issue with the server. Could you try again now that some time has passed?
Are the known keys out of date? Perhaps try running conda update --all

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

j-wags commented 3 years ago

Hi @foxth,

The force field comparison code is currently preliminary -- The big push at this stage is to ensure that everyone can use their in-house computing resources to complete the QM jobs, since that may take > 1 month for large datasets.

Regarding the missing TFD, please do send us the underlying data files You should be able to zip the outputs into a zip or tar.gz file and attach it when replying to this message (you'll have to use github for file attachments, not email). Tagging @dfhahn on this since he's more familiar with the analysis code.

foxth commented 3 years ago

Hi Jeff and David,

 

here the input and output files for the compound for which not all info ends up in the final csv-file. One thing I noticed only now is that your procedure originally created 2 conformations, but only one was successfully calculated - the second one fails with a stereocenter error. Hm.

 

Anyways, please have a look, I cannot exclude that I did sth stupid, although your procedure seemed pretty foolproof to me...

 

Best,

Th.

   

Gesendet: Mittwoch, 27. Januar 2021 um 18:40 Uhr Von: "Jeff Wagner" notifications@github.com An: "openforcefield/openff-benchmark" openff-benchmark@noreply.github.com Cc: "foxth" Thomas.fox@gmx.net, "Mention" mention@noreply.github.com Betreff: Re: [openforcefield/openff-benchmark] Deployment procedure: conda create env fails (#41)

 

Hi @foxth,

The force field comparison code is currently preliminary -- The big push at this stage is to ensure that everyone can use their in-house computing resources to complete the QM jobs, since that may take > 1 month for large datasets.

Regarding the missing TFD, please do send us the underlying data files You should be able to zip the outputs into a zip or tar.gz file and attach it when replying to this message (you'll have to use github for file attachments, not email). Tagging @dfhahn on this since he's more familiar with the analysis code.

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dotsdl commented 3 years ago

here the input and output files for the compound for which not all info ends up in the final csv-file. One thing I noticed only now is that your procedure originally created 2 conformations, but only one was successfully calculated - the second one fails with a stereocenter error. Hm.

Hi @foxth, the file didn't attach because your email gets posted as a comment on this issue. However, I'll note that this failure was for an earlier iteration of the protocol software and it may now be a moot point.

We're still interested in this failure mode, however, since it is odd that one conformer for a molecule failed with a stereocenter error while another succeeded. If you're able to find the failed conformer's SDF file, can you post the contents here (assuming this is a publicly-shareable compound)?