Skip to Content.
Sympa Menu

opal - Re: [Opal] mpirun and anaconda

opal AT lists.psi.ch

Subject: The OPAL Discussion Forum

List archive

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 23:17:31 +0000
  • Accept-language: en-US, de-CH
  • Authentication-results: mc1; iprev=pass (psi-seppmail1.ethz.ch) smtp.remote-ip=129.132.93.141; spf=pass smtp.mailfrom=psi.ch; dmarc=skipped

Hi seongyeol

> On 26 Jan 2022, at 23:43, Kim, Seongyeol <seongyeol.kim AT anl.gov> wrote:
>
> Dear Gsell, Nicole, Alba, Andreas,
>
> Thank you all for your nice help!
> I checked that when I activated the Anaconda, then the path of the mpirun
> is changed to anaconda, not the opal directory.
> Now I understood why it does not work with anaconda environment.
>
> Following Alba's suggestion, I tried to find the line, but I could not find
> it (but thank you for your suggestion!).

Playing with LD_LIBRARY_PATH doesn't help here. In the OPAL package all
binaries and libraries have an explicit RPATH set. This cannot be overwritten
by LD_LIBRARY_PATH. In other words: All binaries in the OPAL package are
using the libraries shipped with the package. Anaconda is doing something
similar and you end up with two completely independent MPI installations.
mpirun shipped with anaconda cannot communicate with the mpirun shipped with
OPAL. The result is the behaviour you observed.

> Then I tried with Gsell's suggestion, ($OPAL_PREFIX/bin/mpirun -np 4 opal
> ....), and I checked it works!
> I am not sure if it works when I remove the mpirun installed in the
> anaconda, but I will try.

You can remove MPI from anaconda, but there is no need for it.

Best,

Achim


>
> Thank you for your help again!
>
> Best regards,
> seongyeol
>
> From: Gsell Achim (PSI) <achim.gsell AT psi.ch>
> Sent: Wednesday, January 26, 2022 15:56
> 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
>
> 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
> > Zoom ID: 470-582-4086 Password: AdA
> > Zoom Link:
> > https://ethz.zoom.us/j/4705824086?pwd=dFcvT1pMMGY0bHg0dTNncUNZZTJkZz09
> >
> > -------------------------------------------------------
> > Friday: ETH HPK G 28 +41 44 633 3076
> > ============================================
> > The more exotic, the more abstract the knowledge,
> > the more profound will be its consequences.
> > Leon Lederman
> > ============================================
> >
> >
> > On 26 Jan 2022, at 19:13, Kim, Seongyeol <seongyeol.kim AT anl.gov> wrote:
> >
> > Seongyeol




Archive powered by MHonArc 2.6.19.

Top of Page