The OPAL Discussion Forum

["Kim, Seongyeol" <seongyeol.kim AT anl.gov>]

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,

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
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>
> On 26 Jan 2022, at 19:13, Kim, Seongyeol <seongyeol.kim AT anl.gov> wrote:
> 
> Seongyeol