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Re: [Opal] mpirun and anaconda

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  • From: "Kim, Seongyeol" < AT>
  • To: "Gsell Achim (PSI)" <achim.gsell AT>
  • Cc: "Adelmann Andreas (PSI)" <andreas.adelmann AT>, "opal AT" <opal AT>, Nicole R Neveu <nneveu AT>
  • Subject: Re: [Opal] mpirun and anaconda
  • Date: Wed, 26 Jan 2022 22:43:38 +0000
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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!).
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.

Thank you for your help again!

Best regards,

From: Gsell Achim (PSI) <achim.gsell AT>
Sent: Wednesday, January 26, 2022 15:56
To: Kim, Seongyeol < AT>
Cc: Adelmann Andreas (PSI) <andreas.adelmann AT>; opal AT <opal AT>; Nicole R Neveu <nneveu AT>
Subject: Re: [Opal] mpirun and anaconda
Hi Seomgyeol

> On 26 Jan 2022, at 22:48, Nicole R Neveu <nneveu AT> 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.



> Thanks,

> Nicole

> From: opal-request AT <opal-request AT> on behalf of Kim, Seongyeol < AT>
> Date: Wednesday, January 26, 2022 at 12:55 PM
> To: Adelmann Andreas (PSI) <andreas.adelmann AT>
> Cc: opal AT <opal AT>
> 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 where indicates the name of the input file.
> For the parallel running, I used: mpirun -np number opal 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>
> Sent: Wednesday, January 26, 2022 14:20
> To: Kim, Seongyeol < AT>
> Cc: opal AT <opal AT>
> 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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> 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 < AT> wrote:

> Seongyeol

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