[Opm] OPM Flow multi-node simulations stuck at domain decomposition step
Yogi Pandey
yogi.pandey at oracle.com
Thu Mar 12 22:31:51 UTC 2020
Installing Eigen 3.1 did not fix it. I am still getting the same error. Any suggestions from the ones who have done it in the past.
OS is Oracle Linux 7 (binary compatible with RHEL).
Thanks.
-----Original Message-----
From: Yogi Pandey
Sent: Thursday, March 12, 2020 5:16 PM
To: Joakim Hove <joakim.hove at gmail.com>; opm at opm-project.org
Subject: Re: [Opm] OPM Flow multi-node simulations stuck at domain decomposition step
Looking at the documentation here: https://urldefense.com/v3/__https://github.com/OPM/opm-simulators/tree/release/2019.10__;!!GqivPVa7Brio!I_1R6MQvXO98YsD--aGpMqnti1zfa63_k1NpHzyDpC9xvLyKlJB9DRRyCv5O-y_MuQ$
It seems I need an additional library Eigen 3.1. Will try with it, and let everyone know how it goes.
Thanks.
-----Original Message-----
From: Yogi Pandey
Sent: Thursday, March 12, 2020 5:01 PM
To: Joakim Hove <joakim.hove at gmail.com>; opm at opm-project.org
Subject: Re: [Opm] OPM Flow multi-node simulations stuck at domain decomposition step
Thank you for your comment. Yes, I already have that step. I had omitted some steps as they are obvious. Here’s the full set of commands for the pre-requisites other than the ones installed from source:
sudo yum install -y devtoolset-8
echo 'source /opt/rh/devtoolset-8/enable' >> ~/.bashrc
echo 'export LD_LIBRARY_PATH=${LD_LIBRARY_PATH-}:/usr/lib64:/usr/local/lib' >> ~/.bashrc
echo 'export C_INCLUDE_PATH=${C_INCLUDE_PATH-}:/usr/local/include' >> ~/.bashrc
source ~/.bashrc
sudo yum install -y gmp gmp-devel
sudo yum install -y lapack lapack-devel
sudo yum install -y suitesparse suitesparse-devel
I have all pre-requisites listed on the current version of this page: https://urldefense.com/v3/__https://opm-project.org/?page_id=239__;!!GqivPVa7Brio!IYx9RG8p2DhjkX4SxQ879dH_7l5fuRJF0MAUx85mPu2C5E9zXsc6fYGHyQv_UFoFMQ$
I was able to build OPM Flow from the latest source using these pre-requisites.
Thank you,
Yogi Pandey, Ph.D.
From: Joakim Hove [mailto:joakim.hove at gmail.com]
Sent: Thursday, March 12, 2020 4:51 PM
To: Yogi Pandey <yogi.pandey at oracle.com>; opm at opm-project.org
Subject: Re: [Opm] OPM Flow multi-node simulations stuck at domain decomposition step
Are you certain that you actually pick up the correct compiler - my guess is that you use the system compiler which is too old.
Try: " source /opt/rh/devtoolset-7/enable" - wipe the build directory and rerun cmake.
Joakim
tor. 12. mar. 2020, 22:17 skrev Yogi Pandey <HYPERLINK "mailto:yogi.pandey at oracle.com%22yogi.pandey at oracle.com>:
Hi Atgeirr,
I've tried building 2019.10 from source. I encountered following error while building opm-common:
[ 6%] Built target genkw
[ 7%] Updating version information
[ 7%] Built target update-version
[ 7%] Building CXX object CMakeFiles/opmcommon.dir/src/opm/parser/eclipse/Parser/Parser.cpp.o
/home/opc/Installers/Opm-Flow-2019.10/opm-common/src/opm/parser/eclipse/Parser/Parser.cpp:311:37: error: expected template-name before ‘<’ token
class InputStack : public std::stack< file, std::vector< file > > {
^
/home/opc/Installers/Opm-Flow-2019.10/opm-common/src/opm/parser/eclipse/Parser/Parser.cpp:311:37: error: expected ‘{’ before ‘<’ token
/home/opc/Installers/Opm-Flow-2019.10/opm-common/src/opm/parser/eclipse/Parser/Parser.cpp:311:37: error: expected unqualified-id before ‘<’ token
/home/opc/Installers/Opm-Flow-2019.10/opm-common/src/opm/parser/eclipse/Parser/Parser.cpp:320:71: error: invalid use of incomplete type ‘class Opm::{anonymous}::InputStack’
void InputStack::push( std::string&& input, boost::filesystem::path p ) {
^
/home/opc/Installers/Opm-Flow-2019.10/opm-common/src/opm/parser/eclipse/Parser/Parser.cpp:311:7: note: forward declaration of ‘class Opm::{anonymous}::InputStack’
class InputStack : public std::stack< file, std::vector< file > > {
^~~~~~~~~~
/home/opc/Installers/Opm-Flow-2019.10/opm-common/src/opm/parser/eclipse/Parser/Parser.cpp:348:20: error: field ‘input_stack’ has incomplete type ‘Opm::{anonymous}::InputStack’
InputStack input_stack;
^~~~~~~~~~~
/home/opc/Installers/Opm-Flow-2019.10/opm-common/src/opm/parser/eclipse/Parser/Parser.cpp:311:7: note: forward declaration of ‘class Opm::{anonymous}::InputStack’
class InputStack : public std::stack< file, std::vector< file > > {
^~~~~~~~~~
make[2]: *** [CMakeFiles/opmcommon.dir/build.make:2728: CMakeFiles/opmcommon.dir/src/opm/parser/eclipse/Parser/Parser.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:1962: CMakeFiles/opmcommon.dir/all] Error 2
make: *** [Makefile:141: all] Error 2
Following is the list of pre-requisites I have (not listing all commands here):
-sudo yum install -y devtoolset-8 (for GCC-8.3.1) -sudo yum install -y gmp gmp-devel -sudo yum install -y lapack lapack-devel -sudo yum install -y suitesparse suitesparse-devel
-openmpi-4.0.2 (built from source)
-boost-1.72.0 (built from source)
-cmake-3.16.4 (built from source)
-parmetis-4.0.3 (built from source)
-dune-2.6.0: dune-common, dune-geometry, dune-grid, dune-istl (built from source)
-Zoltan-3.83 (built from source)
OPM Flow module opm-common is built using following commads:
1) cmake -DCMAKE_BUILD_TYPE=Release -DUSE_MPI=ON -DUSE_OPENMP=ON -DBLAS_LIBRARIES=/usr/lib64 -DCMAKE_INSTALL_PREFIX=/usr/local ..
2) sudo make
Am I missing any pre-requisite?
Any help will be greatly appreciated.
Thank you,
Yogi Pandey, Ph.D.
-----Original Message-----
From: Yogi Pandey
Sent: Wednesday, March 11, 2020 9:59 AM
To: Atgeirr Rasmussen <HYPERLINK "mailto:Atgeirr.Rasmussen at sintef.no%22Atgeirr.Rasmussen at sintef.no>; HYPERLINK "mailto:opm at opm-project.org%22opm at opm-project.org
Subject: RE: [Opm] OPM Flow multi-node simulations stuck at domain decomposition step
Thank you for the suggestion Atgeirr. I'll try out the previous release 2019.10.
- Yogi
-----Original Message-----
From: Atgeirr Rasmussen [mailto:HYPERLINK "mailto:Atgeirr.Rasmussen at sintef.no%22Atgeirr.Rasmussen at sintef.no]
Sent: Wednesday, March 11, 2020 6:46 AM
To: HYPERLINK "mailto:opm at opm-project.org%22opm at opm-project.org
Subject: Re: [Opm] OPM Flow multi-node simulations stuck at domain decomposition step
Hi Yogi,
Lots of things have changed in Flow for the initialization in parallel recently. Could you try to check out the previous release (2019.10) and check if you see the same problems?
Atgeirr
________________________________
Frå: Opm <HYPERLINK "mailto:opm-bounces at opm-project.org%22opm-bounces at opm-project.org> på vegne av Markus Blatt <HYPERLINK "mailto:markus at dr-blatt.de%22markus at dr-blatt.de>
Sendt: onsdag 11. mars 2020 11:08
Til: HYPERLINK "mailto:opm at opm-project.org%22opm at opm-project.org <HYPERLINK "mailto:opm at opm-project.org%22opm at opm-project.org>
Emne: Re: [Opm] OPM Flow multi-node simulations stuck at domain decomposition step
Hi Yogi,
On Tue, Mar 10, 2020 at 02:15:19PM -0700, Yogi Pandey wrote:
> Simulation is being run on 4 nodes with 32 processors each using following command:
>
> mpirun --display-map -mca btl self -x UCX_TLS=rc,self,sm -x
> HCOLL_ENABLE_MCAST_ALL=0 -mca coll_hcoll_enable 0 -x
> UCX_IB_TRAFFIC_CLASS=105 -x UCX_IB_GID_INDEX=3 --cpu-set
> 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26
> ,27,28,29,30,31,32,33,34,35 -np 144 --hostfile /etc/opt/rdma/hostfile
> /mnt/nfs-share/etc/opm-flow/opm-simulators/build/bin/flow
> --parameter-file=/mnt/nfs-share/data/norne/params
>
Out of curiosity. Is there a special reason why --cpu-set runs until 35 with 32 cpus per node? Might you be oversubscribing a node?
Markus
--
Dr. Markus Blatt
OPM-OP AS
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