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Re: [Opal] mpirun and anaconda


Chronological Thread  
  • From: "Gsell Achim (PSI)" <achim.gsell AT psi.ch>
  • To: "Kim, Seongyeol" <seongyeol.kim AT anl.gov>
  • Cc: "Adelmann Andreas (PSI)" <andreas.adelmann AT psi.ch>, "opal AT lists.psi.ch" <opal AT lists.psi.ch>, Nicole R Neveu <nneveu AT stanford.edu>
  • Subject: Re: [Opal] mpirun and anaconda
  • Date: Wed, 26 Jan 2022 21:56:05 +0000
  • Accept-language: en-US, de-CH
  • Authentication-results: mc4.ethz.ch; iprev=pass (psi-seppmail1.ethz.ch) smtp.remote-ip=129.132.93.141; spf=pass smtp.mailfrom=psi.ch; dmarc=skipped

Hi Seomgyeol

> On 26 Jan 2022, at 22:48, Nicole R Neveu <nneveu AT stanford.edu> wrote:
>
> Hi Seongyeol,
>
> Maybe you have accidentally installed another mpi in your conda environment.
> This happened to me recently. You can check with mpi you are using by
> calling:
> >which mpirun
>
> See if you get the same results w/ and w/o your conda env loaded.

Yes, most likely. You should use mpirun from the OPAL package:

$OPAL_PREFIX/bin/mpirun -np 4 opal ....

If this doesn't work, please send the output of

ldd $OPAL_PREFIX/bin/opal

before and after loading anaconda. Sourcing the OPAL profile after
initialising anaconda might also help.

Best

Achim


>
> Thanks,
>
> Nicole
>
> From: opal-request AT lists.psi.ch <opal-request AT lists.psi.ch> on behalf of
> Kim, Seongyeol <seongyeol.kim AT anl.gov>
> Date: Wednesday, January 26, 2022 at 12:55 PM
> To: Adelmann Andreas (PSI) <andreas.adelmann AT psi.ch>
> Cc: opal AT lists.psi.ch <opal AT lists.psi.ch>
> Subject: Re: [Opal] mpirun and anaconda
>
> Dear Andreas,
>
> Please find the attached pdf file for more details.
>
> When calling the OPAL, I simply used: opal input.in where input.in
> indicates the name of the input file.
> For the parallel running, I used: mpirun -np number opal input.in. Here I
> put the number to 4 just in case for checking.
>
> Indeed, when I activate the Anaconda through .bashrc, you can see that
> there are 4 same messages when I try to do parallel run.
> On the other hand, when I deactivate the Anaconda, then it works fine. This
> also happens when using miniconda.
>
> Thank you for your help!
> Best regards,
> Seongyeol
> From: Adelmann Andreas (PSI) <andreas.adelmann AT psi.ch>
> Sent: Wednesday, January 26, 2022 14:20
> To: Kim, Seongyeol <seongyeol.kim AT anl.gov>
> Cc: opal AT lists.psi.ch <opal AT lists.psi.ch>
> Subject: Re: [Opal] mpirun and anaconda
>
> Dear Seongyeol to me this is an incompatibility with the MPI library
> OPAL is build with and, your Anaconda/Python installation.
>
> Can you elaborate a bit more how you call OPAL for the notebook?
>
> Cheers A
> ------
> Dr. sc. math. Andreas (Andy) Adelmann
> Head a.i. Labor for Scientific Computing and Modelling
> Paul Scherrer Institut OHSA/ CH-5232 Villigen PSI
> Phone Office: xx41 56 310 42 33 Fax: xx41 56 310 31 91
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>
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> ============================================
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> the more profound will be its consequences.
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>
>
> On 26 Jan 2022, at 19:13, Kim, Seongyeol <seongyeol.kim AT anl.gov> wrote:
>
> Seongyeol




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