[Opm] OPM Flow RedHat 7 Binary Package Build with MPI Support

Mon May 7 06:13:14 UTC 2018

hi,

i suspect you have not enabled the epel repo (extra packages for enterprise linux). epel is required.

arnem

________________________________
Fra: Opm <opm-bounces at opm-project.org> på vegne av sindimo <sindimo at gmail.com>
Sendt: mandag 7. mai 2018 01.56.37
Til: Alf Birger Rustad; Arne Morten Kvarving; opm at opm-project.org
Emne: Re: [Opm] OPM Flow RedHat 7 Binary Package Build with MPI Support

Dear Arne and Alf,

Thank you for the clarifications.

I am using the below yum repo found on the OPM website when doing the installation. When installing the opm-simulators-openmpi-bin package to get the mpi binaries it fails to install with the below errors related to dependencies of trilinos. Is there another missing yum repo that I need to add to resolve these broken dependencies?

Many thanks!

sudo yum-config-manager --add-repo http://www.opm-project.org/package/opm.repo

sudo yum install opm-simulators-bin                         <-----This installs fine

sudo yum install opm-simulators-openmpi-bin          <-----This fails

--> Finished Dependency Resolution
Error: Package: trilinos-11.2.5-1.12.x86_64 (opm)
           Requires: libscotcherr.so.0()(64bit)
Error: Package: trilinos-11.2.5-1.12.x86_64 (opm)
           Requires: libscotch.so.0()(64bit)
Error: Package: trilinos-11.2.5-1.12.x86_64 (opm)
           Requires: libdmumps-5.1.2.so<http://libdmumps-5.1.2.so>()(64bit)
Error: Package: libopm-simulators1-openmpi-2018.04-0.x86_64 (opm)
           Requires: libptscotcherr.so.0()(64bit)
Error: Package: libopm-simulators1-openmpi-2018.04-0.x86_64 (opm)
           Requires: libptscotch.so.0()(64bit)
Error: Package: libopm-simulators1-openmpi-2018.04-0.x86_64 (opm)
           Requires: libscotch.so.0()(64bit)
Error: Package: trilinos-11.2.5-1.12.x86_64 (opm)
           Requires: libglpk.so.36()(64bit)
Error: Package: opm-simulators-openmpi-bin-2018.04-0.x86_64 (opm)
           Requires: libptscotcherr.so.0()(64bit)
Error: Package: opm-simulators-openmpi-bin-2018.04-0.x86_64 (opm)
           Requires: libscotch.so.0()(64bit)
Error: Package: opm-simulators-openmpi-bin-2018.04-0.x86_64 (opm)
           Requires: libptscotch.so.0()(64bit)
Error: Package: trilinos-11.2.5-1.12.x86_64 (opm)
           Requires: libpord-5.1.2.so<http://libpord-5.1.2.so>()(64bit)
Error: Package: trilinos-11.2.5-1.12.x86_64 (opm)
           Requires: libhdf5.so.8()(64bit)

On Fri, May 4, 2018 at 6:18 AM, Alf Birger Rustad <abir at statoil.com<mailto:abir at statoil.com>> wrote:

Hi Mohamad,

As Arne Morten says, you will need to tell Red Hat what MPI version to use. The way this is done is by first making the module command available. You achieve this by the following command:

. /usr/share/Modules/init/bash

Now you can query for installed modules with:

module avail

Lastly, you can tell it to use openmpi with:

module add mpi/openmpi-x86_64

On ubuntu, you do not need to do anything. If openmpi is installed, mpirun just works.

Cheers,

Alf

From: Opm [mailto:opm-bounces at opm-project.org<mailto:opm-bounces at opm-project.org>] On Behalf Of Arne Morten Kvarving
Sent: 4. mai 2018 11:22
To: sindimo <sindimo at gmail.com<mailto:sindimo at gmail.com>>; opm at opm-project.org<mailto:opm at opm-project.org>
Subject: Re: [Opm] OPM Flow RedHat 7 Binary Package Build with MPI Support

hi there,

on redhat things work a little different. in particular there are separate packages for mpi.

you have to install opm-simulators-openmpi-bin

and load the mpi/openmpi-x86_64 module in the shell where you want to execute flow.

arnem

________________________________

Fra: saudiaramco at gmail.com<mailto:saudiaramco at gmail.com> <saudiaramco at gmail.com<mailto:saudiaramco at gmail.com>> på vegne av sindimo <sindimo at gmail.com<mailto:sindimo at gmail.com>>
Sendt: 4. mai 2018 11:15:36
Til: Arne Morten Kvarving; opm at opm-project.org<mailto:opm at opm-project.org>
Emne: Re: [Opm] OPM Flow RedHat 7 Binary Package Build with MPI Support

Hi Arne,

Thank you for your clarification, I really appreciate it.

I have updated to the latest OPM release of Flow 2018.04 and tested again on RedHat 7. I still don't see any performance improvement with the new RedHat 7 binaries as if MPI was still not working. On Ubuntu it works fine.

For example I ran the Norne model once on 1 processor and once on 2 processors on the RedHat 7 machine and the Ubuntu machine (identical machines on Amazon AWS m4.2xlarge instances) and these are the timings I get:

Norne on RedHat:

1 processor:  769.437 seconds

2 processors: 839.285 seconds

Norne on Ubuntu:

1 processor:  889.158 seconds

2 processors: 585 seconds

If I do "top" command on RedHat while job is launched on 2 processors, I can see 2 processors running. However it doesn't seem that they are running in parallel, it seems as if each process is running a separate serial copy of flow, hence the run on 2 processors is even slower than the serial run.

Also a quick check using "ldd" on the flow binaries on both Ubuntu and RedHat shows that the Ubuntu executable is indeed linked to the MPI library, while the RedHat binary still doesn't show any linked MPI libraries:

On Ubuntu:

ubuntu at ip-172-31-15-200:~$ ldd /usr/bin/flow | grep -i mpi

libmpi_cxx.so.1 => /usr/lib/libmpi_cxx.so.1 (0x00007f350423c000)

libmpi.so.12 => /usr/lib/libmpi.so.12 (0x00007f3503f66000)

On RedHat:

[ec2-user at ip-172-31-15-201 ~]$ ldd /usr/bin/flow | grep mpi

[ec2-user at ip-172-31-15-201 ~]$

[ec2-user at ip-172-31-15-201 ~]$ rpm -qa | grep opm

libopm-common1-2018.04-0.x86_64

opm-upscaling-devel-2018.04-0.x86_64

opm-simulators-bin-2018.04-0.x86_64

libopm-grid1-2018.04-0.x86_64

libopm-upscaling1-2018.04-0.x86_64

libopm-simulators1-2018.04-0.x86_64

opm-upscaling-2018.04-0.x86_64

I would appreciate any help with this please to get the parallel version of Flow working on RedHat.

Thank you for all of your help.

Sincerely,

Mohamad

On Thu, Apr 26, 2018 at 2:26 AM, Arne Morten Kvarving <Arne.Morten.Kvarving at sintef.no<mailto:Arne.Morten.Kvarving at sintef.no>> wrote:

hi,

currently the rpm's are not mpi enabled. this will change in the upcoming 2018.04 release.

it's a bit involved building on rhel, as you need some packages not in base or epel. in particular, you need to trilinos (or rather, just zoltan which is part of trilinos) to get efficient mpi support, as well as dune and such. if it's not extremely pressing i would suggest waiting for the release.

arnem

________________________________

Fra: Opm <opm-bounces at opm-project.org<mailto:opm-bounces at opm-project.org>> på vegne av M. S. <sindimo at gmail.com<mailto:sindimo at gmail.com>>
Sendt: 25. april 2018 22:46:33
Til: opm at opm-project.org<mailto:opm at opm-project.org>
Emne: [Opm] OPM Flow RedHat 7 Binary Package Build with MPI Support

Dear All,

I am interested in running OPM Flow with MPI support on RedHat 7.

I've installed the binary packages on 2 different machines, one with RedHat 7 and the other with Ubuntu 16.04 using these instructions:

https://opm-project.org/?page_id=245

The Ubuntu packages ran fine with MPI and I can see performance improvement when running some of the SPE models, however the RedHat 7 version doesn't seem to have been built with MPI support.

RedHat 7 currently has native mpi package that can be easily installed by yum (based on mpich-3):

sudo yum -y install mpich-devel

Would someone be able please to build the Flow binaries for RedHat 7 with MPI support, or perhaps if they already exist can you please point me to where to get them?

I attempted building from source code but the Flow third party library prerequisite installation seems overwhelming.

If anyone already has their RedHat 7 build environment setup and would be able to help I would truly appreciate it. From the instructions on the website, it says to enable MPI support you just need to pass this option to cmake during the build “-DUSE_MPI=1” .

Thank you for all of your help, I really appreciate it.

Sincerely,

Mohamad Sindi

MIT

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