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CCPEM  June 2020

CCPEM June 2020

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Subject:

Re: MPI runtime errors - RELION 3.0 and 3.1 on CentOS 8.1

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Mon, 1 Jun 2020 21:11:54 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (151 lines)

Hi,

It is documented.

 > Probably you are using a version of MPI runtime different from the 
one used during compilation.

https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#Program_crashes_showing_MPI_runtime_errors

 > The MPI library must be the one you intend to use RELION with. 
Compiling RELION with one version of MPI and running the resulting 
binary with mpirun from another version can cause crash.

https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Download_%26_install#Installing_from_source_code

 > I am pretty sure I compiled and ran with the same MPI,
 > because I only have one version installed.

This assumption was not correct, as 3.1 was used to
compile while 4.0 was used to run.

Best regards,

Takanori Nakane

On 2020/06/01 16:54, Guillaume Gaullier wrote:
> I installed OpenMPI 3.1 and now it works fine. It would be helpful if 
> this version compatibility thing was documented in the wiki.
> Cheers,
> 
> Guillaume
> 
> 
>> On 1 Jun 2020, at 15:34, Takanori Nakane <[log in to unmask] 
>> <mailto:[log in to unmask]>> wrote:
>>
>> Hi,
>>
>> RELION does work with OpenMPI 3.x.
>>
>> Your problem is that you compiled RELION with
>> OpenMPI 3.1 but running it with mpirun version
>> 4.0.1.
>>
>> I don't know why cmake picked up OpenMPI 3.1,
>> because your "module" layer might have changed many
>> environmental variables.
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2020/06/01 14:27, Guillaume Gaullier wrote:
>>> Hi,
>>> True, but I don’t really understand why that is. In a fresh bash 
>>> session, `which mpirun` returns nothing, so I load the system mpi 
>>> modulefile, then I have an mpirun in PATH and when I run mpirun 
>>> --version I get 4.0.1, which is consistent with what the system 
>>> package manager reports for my installed version of OpenMPI.
>>> When I compile RELION, I also load the system mpi modulefile before 
>>> running cmake, make and make install. If I don’t load this 
>>> modulefile, cmake reports it can’t find any MPI (which is also 
>>> consistent with the observations above).
>>> Is RELION not compatible with OpenMPI 3.1? And if so, how do I make 
>>> my system-installed OpenMPI 4.0.1 detected and used properly?
>>> Have you looked at the run.err and can you exclude this is a bug in 
>>> RELION?
>>> Thank you,
>>> Guillaume
>>>> On 1 Jun 2020, at 15:09, Takanori Nakane <[log in to unmask] 
>>>> <mailto:[log in to unmask]> 
>>>> <mailto:[log in to unmask]>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> You said OpenMPI 4.0.1 but your cmake log says
>>>> > -- Found MPI_C: /usr/lib64/openmpi/lib/libmpi.so (found version "3.1")
>>>>
>>>> Best regards,
>>>>
>>>> Takanori Nakane
>>>>
>>>> On 2020/06/01 14:01, Guillaume Gaullier wrote:
>>>>> Hello CCPEM,
>>>>> I installed RELION 3.0 (commit 
>>>>> 5a8f82785e53bc8ed271b096c3f7afff09e5e82f ) and also the latest in 
>>>>> branch 3.1 (commit 5997001f75abd0f1fa135ee25e04f92c855e5e29 ). They 
>>>>> compile and install fine on a fresh CentOS 8.1, but I get MPI 
>>>>> errors at runtime with both versions of RELION. I attached a 
>>>>> run.err obtained with RELION 3.1 while trying to go through the 
>>>>> tutorial.
>>>>> I did read the FAQ about MPI runtime errors ( 
>>>>> https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#Program_crashes_showing_MPI_runtime_errors 
>>>>> ), and I am pretty sure I compiled and ran with the same MPI, 
>>>>> because I only have one version installed. It is OpenMPI 4.0.1, 
>>>>> installed with the distribution’s package manager. I also believe 
>>>>> the environment is correctly set up both during compilation and at 
>>>>> run time, because I use the environment modules system and I use 
>>>>> the modulefile provided by the system installation of OpenMPI. I 
>>>>> also tested the mpirun command with unrelated programs, and it 
>>>>> worked as expected.
>>>>> So, as far as I can tell, this looks like either a bug in RELION or 
>>>>> an incompatibility with this version of OpenMPI (if so, it would be 
>>>>> very helpful to list compatible versions of OpenMPI on the wiki).
>>>>> I would be happy to be told I messed something up during 
>>>>> installation and there is an easy fix, so I also attached the 
>>>>> output of my fresh cmake just in case it would point to a problem 
>>>>> with my installation.
>>>>> Can someone help me with this issue?
>>>>> Thank you in advance,
>>>>> Guillaume
>>>>> ########################################################################
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