[Opm] OPM Flow multi-node simulations stuck at domain decomposition step
Bård Skaflestad
Bard.Skaflestad at sintef.no
Thu Mar 12 23:39:57 UTC 2020
Hi,
To be honest, it really looks like you've hit a bug in OPM. The diagnostic messages suggest that the templated type 'std::stack' is not defined in this scope, which would mean that we've failed to
#include <stack>
somewhere we should have. True enough, the source file
opm-common/src/opm/parser/eclipse/Parser/Parser.cpp
definitely does not include <stack>. What's more, I don't find a trace of having included <stack> anywhere in our source base which makes me question how this could ever have compiled for anyone. I do suppose that it's possible for some other standard header to pull in a declaration of std::stack, but then we would have been really unlucky for a long time.
That said, the only use I can find of the class std::stack is in Parser.cpp, so that file should include the header directly.
Would you mind trying to add
#include <stack>
to the source file in question to see if that solves--or at least alleviates--the problem?
Best Regards,
Bård Skaflestad
SINTEF Digital, Mathematics & Cybernetics
Computational Geosciences group
-----Original Message-----
From: Opm <opm-bounces at opm-project.org> On Behalf Of Yogi Pandey
Sent: Thursday, March 12, 2020 6:14 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
After looking at https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOPM%2Fopm-simulators%2Fblob%2Frelease%2F2019.10%2Fopm-simulators-prereqs.cmake&data=02%7C01%7CBard.Skaflestad%40sintef.no%7Ccc22ff05a90a4d87df1508d7c6dadac9%7Ce1f00f39604145b0b309e0210d8b32af%7C1%7C1%7C637196515588832188&sdata=eOS%2BFNKNPch%2FrSIUu%2BkY7I7%2Fm%2BC%2BudkcHcVMpkufye8%3D&reserved=0, I added SuperLU -6.1.1 and libecl to the dependencies. I still have the same error:
[ 32%] 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
Any help will be appreciated.
Thank you.
-----Original Message-----
From: Yogi Pandey
Sent: Thursday, March 12, 2020 5:32 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
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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fgithub.com%2FOPM%2Fopm-simulators%2Ftree%2Frelease%2F2019.10__%3B!!GqivPVa7Brio!I_1R6MQvXO98YsD--aGpMqnti1zfa63_k1NpHzyDpC9xvLyKlJB9DRRyCv5O-y_MuQ%24&data=02%7C01%7CBard.Skaflestad%40sintef.no%7Ccc22ff05a90a4d87df1508d7c6dadac9%7Ce1f00f39604145b0b309e0210d8b32af%7C1%7C0%7C637196515588832188&sdata=Y6Op%2FrZpqwwgt1t%2FzGuVcF12wbeR%2Bgg1mb%2FhCNMryUs%3D&reserved=0
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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fopm-project.org%2F%3Fpage_id%3D239__%3B!!GqivPVa7Brio!IYx9RG8p2DhjkX4SxQ879dH_7l5fuRJF0MAUx85mPu2C5E9zXsc6fYGHyQv_UFoFMQ%24&data=02%7C01%7CBard.Skaflestad%40sintef.no%7Ccc22ff05a90a4d87df1508d7c6dadac9%7Ce1f00f39604145b0b309e0210d8b32af%7C1%7C0%7C637196515588842183&sdata=2f5f3UqevfPwF6BMV2FztDCLf1NmECDtytskB6j%2FM2E%3D&reserved=0
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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