"Open MPI does not work when MPICH or intel MPI are installed"
Thank you for your suggestion. But I need to run OpenFoam and Empire
at the same time. In fact, Empire couples OpenFoam with another software.
Is there any solution for this case ?
Regards,
Islem
Le Lundi 23 mai 2016 17h00, "users-requ...@open-mpi.org"
<users-requ...@open-mpi.org> a écrit :
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Today's Topics:
1. Re: Open MPI does not work when MPICH or intel MPI are
installed (Andy Riebs)
2. segmentation fault for slot-list and openmpi-1.10.3rc2
(Siegmar Gross)
3. Re: problem about mpirun on two nodes (Jeff Squyres (jsquyres))
4. Re: Open MPI does not work when MPICH or intel MPI are
installed (Gilles Gouaillardet)
5. Re: segmentation fault for slot-list and openmpi-1.10.3rc2
(Ralph Castain)
6. mpirun java (Claudio Stamile)
----------------------------------------------------------------------
[Message discarded by content filter]
------------------------------
Message: 2
Date: Mon, 23 May 2016 15:26:52 +0200
From: Siegmar Gross <siegmar.gr...@informatik.hs-fulda.de>
To: Open MPI Users <us...@open-mpi.org>
Subject: [OMPI users] segmentation fault for slot-list and
openmpi-1.10.3rc2
Message-ID:
<241613b1-ada6-292f-eeb9-722fc8fa2...@informatik.hs-fulda.de>
Content-Type: text/plain; charset=utf-8; format=flowed
Hi,
I installed openmpi-1.10.3rc2 on my "SUSE Linux Enterprise Server
12 (x86_64)" with Sun C 5.13 and gcc-6.1.0. Unfortunately I get
a segmentation fault for "--slot-list" for one of my small programs.
loki spawn 119 ompi_info | grep -e "OPAL repo revision:" -e "C
compiler absolute:"
OPAL repo revision: v1.10.2-201-gd23dda8
C compiler absolute: /usr/local/gcc-6.1.0/bin/gcc
loki spawn 120 mpiexec -np 1 --host loki,loki,loki,loki,loki spawn_master
Parent process 0 running on loki
I create 4 slave processes
Parent process 0: tasks in MPI_COMM_WORLD: 1
tasks in COMM_CHILD_PROCESSES local group: 1
tasks in COMM_CHILD_PROCESSES remote group: 4
Slave process 0 of 4 running on loki
Slave process 1 of 4 running on loki
Slave process 2 of 4 running on loki
spawn_slave 2: argv[0]: spawn_slave
Slave process 3 of 4 running on loki
spawn_slave 0: argv[0]: spawn_slave
spawn_slave 1: argv[0]: spawn_slave
spawn_slave 3: argv[0]: spawn_slave
loki spawn 121 mpiexec -np 1 --host loki --slot-list 0:0-5,1:0-5
spawn_master
Parent process 0 running on loki
I create 4 slave processes
[loki:17326] *** Process received signal ***
[loki:17326] Signal: Segmentation fault (11)
[loki:17326] Signal code: Address not mapped (1)
[loki:17326] Failing at address: 0x8
[loki:17326] [ 0] /lib64/libpthread.so.0(+0xf870)[0x7f4e469b3870]
[loki:17326] [ 1] *** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[loki:17324] Local abort before MPI_INIT completed successfully; not
able to
aggregate error messages, and not able to guarantee that all other
processes
were killed!
/usr/local/openmpi-1.10.3_64_gcc/lib64/libmpi.so.12(ompi_proc_self+0x35)[0x7f4e46c165b0]
[loki:17326] [ 2]
/usr/local/openmpi-1.10.3_64_gcc/lib64/libmpi.so.12(ompi_comm_init+0x68b)[0x7f4e46bf5b08]
[loki:17326] [ 3] *** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[loki:17325] Local abort before MPI_INIT completed successfully; not
able to
aggregate error messages, and not able to guarantee that all other
processes
were killed!
/usr/local/openmpi-1.10.3_64_gcc/lib64/libmpi.so.12(ompi_mpi_init+0xa90)[0x7f4e46c1be8a]
[loki:17326] [ 4]
/usr/local/openmpi-1.10.3_64_gcc/lib64/libmpi.so.12(MPI_Init+0x180)[0x7f4e46c5828e]
[loki:17326] [ 5] spawn_slave[0x40097e]
[loki:17326] [ 6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f4e4661db05]
[loki:17326] [ 7] spawn_slave[0x400a54]
[loki:17326] *** End of error message ***
-------------------------------------------------------
Child job 2 terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero
status, thus
causing
the job to be terminated. The first process to do so was:
Process name: [[56340,2],0]
Exit code: 1
--------------------------------------------------------------------------
loki spawn 122
I would be grateful, if somebody can fix the problem. Thank you
very much for any help in advance.
Kind regards
Siegmar
------------------------------
Message: 3
Date: Mon, 23 May 2016 14:13:11 +0000
From: "Jeff Squyres (jsquyres)" <jsquy...@cisco.com>
To: "Open MPI User's List" <us...@open-mpi.org>
Subject: Re: [OMPI users] problem about mpirun on two nodes
Message-ID: <b2033c1d-8aa4-4823-b984-92756dc1e...@cisco.com>
Content-Type: text/plain; charset="us-ascii"
On May 21, 2016, at 11:31 PM, dour...@aol.com wrote:
>
> I encountered a problem about mpirun and SSH when using OMPI 1.10.0
compiled with gcc, running on centos7.2.
> When I execute mpirun on my 2 node cluster, I get the following
errors pasted below.
>
> [douraku@master home]$ mpirun -np 12 a.out
> Permission denied (publickey,gssapi-keyex,gssapi-with-mic).
This is the key right here: you got a permission denied error when you
(assumedly) tried to execute on the remote server.
Triple check your ssh settings to ensure that you can run on the
remote server(s) without a password or interactive passphrase entry.
--
Jeff Squyres
jsquy...@cisco.com
For corporate legal information go to:
http://www.cisco.com/web/about/doing_business/legal/cri/
------------------------------
Message: 4
Date: Mon, 23 May 2016 23:31:30 +0900
From: Gilles Gouaillardet <gilles.gouaillar...@gmail.com>
To: Open MPI Users <us...@open-mpi.org>
Subject: Re: [OMPI users] Open MPI does not work when MPICH or intel
MPI are installed
Message-ID:
<CAAkFZ5u86Q0ev=ospehnKvd0kumYBoeMD8WF=j+taduh3xy...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
modules are way more friendly that manually setting and exporting your
environment.
the issue here is you are setting your environment in your .bashrc, and
that cannot work if your account is used with various MPI implementations.
(unless your .bashrc checks a third party variable to select the
appropriate mpi, in this case, simply extend the logic to select openmpi)
if you configure'd with --enable-mpirun-prefix-by-default, you should not
need anything in your environment.
Cheers,
Gilles
On Monday, May 23, 2016, Andy Riebs <andy.ri...@hpe.com> wrote:
> Hi,
>
> The short answer: Environment module files are probably the best
solution
> for your problem.
>
> The long answer: See
> <http://www.admin-magazine.com/HPC/Articles/Environment-Modules>
> <http://www.admin-magazine.com/HPC/Articles/Environment-Modules>, which
> pretty much addresses your question.
>
> Andy
>
> On 05/23/2016 07:40 AM, Megdich Islem wrote:
>
> Hi,
>
> I am using 2 software, one is called Open Foam and the other called
EMPIRE
> that need to run together at the same time.
> Open Foam uses Open MPI implementation and EMPIRE uses either MPICH or
> intel mpi.
> The version of Open MPI that comes with Open Foam is 1.6.5.
> I am using Intel (R) MPI Library for linux * OS, version 5.1.3 and MPICH
> 3.0.4.
>
> My problem is when I have the environment variables of either mpich or
> Intel MPI sourced to bashrc, I fail to run a case of Open Foam with
> parallel processing ( You find attached a picture of the error I got )
> This is an example of a command line I use to run Open Foam
> mpirun -np 4 interFoam -parallel
>
> Once I keep the environment variable of OpenFoam only, the parallel
> processing works without any problem, so I won't be able to run EMPIRE.
>
> I am sourcing the environment variables in this way:
>
> For Open Foam:
> source /opt/openfoam30/etc/bashrc
>
> For MPICH 3.0.4
>
> export PATH=/home/islem/Desktop/mpich/bin:$PATH
> export LD_LIBRARY_PATH="/home/islem/Desktop/mpich/lib/:$LD_LIBRARY_PATH"
> export MPICH_F90=gfortran
> export MPICH_CC=/opt/intel/bin/icc
> export MPICH_CXX=/opt/intel/bin/icpc
> export MPICH-LINK_CXX="-L/home/islem/Desktop/mpich/lib/ -Wl,-rpath
> -Wl,/home/islem/Desktop/mpich/lib -lmpichcxx -lmpich -lopa -lmpl -lrt
> -lpthread"
>
> For intel
>
> export PATH=$PATH:/opt/intel/bin/
> LD_LIBRARY_PATH="/opt/intel/lib/intel64:$LD_LIBRARY_PATH"
> export LD_LIBRARY_PATH
> source
>
/opt/intel/compilers_and_libraries_2016.3.210/linux/mpi/intel64/bin/mpivars.sh
> intel64
>
> If Only Open Foam is sourced, mpirun --version gives OPEN MPI (1.6.5)
> If Open Foam and MPICH are sourced, mpirun --version gives mpich 3.0.1
> If Open Foam and intel MPI are sourced, mpirun --version gives intel (R)
> MPI libarary for linux, version 5.1.3
>
> My question is why I can't have two MPI implementation installed and
> sourced together. How can I solve the problem ?
>
> Regards,
> Islem Megdiche
>
>
>
>
>
>
> _______________________________________________
> users mailing listus...@open-mpi.org
<javascript:_e(%7B%7D,'cvml','us...@open-mpi.org');>
> Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users
> Link to this post:
http://www.open-mpi.org/community/lists/users/2016/05/29279.php
>
>
>
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Message: 5
Date: Mon, 23 May 2016 08:45:53 -0700
From: Ralph Castain <r...@open-mpi.org>
To: Open MPI Users <us...@open-mpi.org>
Subject: Re: [OMPI users] segmentation fault for slot-list and
openmpi-1.10.3rc2
Message-ID: <73195d72-cea7-4afc-9527-8f725c8b1...@open-mpi.org>
Content-Type: text/plain; charset="utf-8"
I cannot replicate the problem - both scenarios work fine for me. I?m
not convinced your test code is correct, however, as you call
Comm_free the inter-communicator but didn?t call Comm_disconnect.
Checkout the attached for a correct code and see if it works for you.
FWIW: I don?t know how many cores you have on your sockets, but if you
have 6 cores/socket, then your slot-list is equivalent to ??bind-to
none? as the slot-list applies to every process being launched
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> On May 23, 2016, at 6:26 AM, Siegmar Gross
<siegmar.gr...@informatik.hs-fulda.de> wrote:
>
> Hi,
>
> I installed openmpi-1.10.3rc2 on my "SUSE Linux Enterprise Server
> 12 (x86_64)" with Sun C 5.13 and gcc-6.1.0. Unfortunately I get
> a segmentation fault for "--slot-list" for one of my small programs.
>
>
> loki spawn 119 ompi_info | grep -e "OPAL repo revision:" -e "C
compiler absolute:"
> OPAL repo revision: v1.10.2-201-gd23dda8
> C compiler absolute: /usr/local/gcc-6.1.0/bin/gcc
>
>
> loki spawn 120 mpiexec -np 1 --host loki,loki,loki,loki,loki
spawn_master
>
> Parent process 0 running on loki
> I create 4 slave processes
>
> Parent process 0: tasks in MPI_COMM_WORLD: 1
> tasks in COMM_CHILD_PROCESSES local group: 1
> tasks in COMM_CHILD_PROCESSES remote group: 4
>
> Slave process 0 of 4 running on loki
> Slave process 1 of 4 running on loki
> Slave process 2 of 4 running on loki
> spawn_slave 2: argv[0]: spawn_slave
> Slave process 3 of 4 running on loki
> spawn_slave 0: argv[0]: spawn_slave
> spawn_slave 1: argv[0]: spawn_slave
> spawn_slave 3: argv[0]: spawn_slave
>
>
>
>
> loki spawn 121 mpiexec -np 1 --host loki --slot-list 0:0-5,1:0-5
spawn_master
>
> Parent process 0 running on loki
> I create 4 slave processes
>
> [loki:17326] *** Process received signal ***
> [loki:17326] Signal: Segmentation fault (11)
> [loki:17326] Signal code: Address not mapped (1)
> [loki:17326] Failing at address: 0x8
> [loki:17326] [ 0] /lib64/libpthread.so.0(+0xf870)[0x7f4e469b3870]
> [loki:17326] [ 1] *** An error occurred in MPI_Init
> *** on a NULL communicator
> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> *** and potentially your MPI job)
> [loki:17324] Local abort before MPI_INIT completed successfully; not
able to aggregate error messages, and not able to guarantee that all
other processes were killed!
>
/usr/local/openmpi-1.10.3_64_gcc/lib64/libmpi.so.12(ompi_proc_self+0x35)[0x7f4e46c165b0]
> [loki:17326] [ 2]
/usr/local/openmpi-1.10.3_64_gcc/lib64/libmpi.so.12(ompi_comm_init+0x68b)[0x7f4e46bf5b08]
> [loki:17326] [ 3] *** An error occurred in MPI_Init
> *** on a NULL communicator
> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> *** and potentially your MPI job)
> [loki:17325] Local abort before MPI_INIT completed successfully; not
able to aggregate error messages, and not able to guarantee that all
other processes were killed!
>
/usr/local/openmpi-1.10.3_64_gcc/lib64/libmpi.so.12(ompi_mpi_init+0xa90)[0x7f4e46c1be8a]
> [loki:17326] [ 4]
/usr/local/openmpi-1.10.3_64_gcc/lib64/libmpi.so.12(MPI_Init+0x180)[0x7f4e46c5828e]
> [loki:17326] [ 5] spawn_slave[0x40097e]
> [loki:17326] [ 6]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f4e4661db05]
> [loki:17326] [ 7] spawn_slave[0x400a54]
> [loki:17326] *** End of error message ***
> -------------------------------------------------------
> Child job 2 terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
> -------------------------------------------------------
>
--------------------------------------------------------------------------
> mpiexec detected that one or more processes exited with non-zero
status, thus causing
> the job to be terminated. The first process to do so was:
>
> Process name: [[56340,2],0]
> Exit code: 1
>
--------------------------------------------------------------------------
> loki spawn 122
>
>
>
>
> I would be grateful, if somebody can fix the problem. Thank you
> very much for any help in advance.
>
>
> Kind regards
>
> Siegmar
> _______________________________________________
> users mailing list
> us...@open-mpi.org
> Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users
> Link to this post:
http://www.open-mpi.org/community/lists/users/2016/05/29281.php
------------------------------
Message: 6
Date: Mon, 23 May 2016 17:47:53 +0200
From: Claudio Stamile <claudiostam...@gmail.com>
To: us...@open-mpi.org
Subject: [OMPI users] mpirun java
Message-ID:
<caadd79zz1waonmr5hod3jp51qeduhmp5ww8tp7eujldfshe...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear all,
I'm using openmpi for Java.
I've a problem when I try to use more option parameters in my java
command.
More in detail I run mpirun as follow:
mpirun -n 5 java -cp path1:path2 -Djava.library.path=pathLibs
classification.MyClass
It seems that the option "-Djava.library.path" is ignored when i execute
the command.
Is it normal ?
Do you know how to solve this problem ?
Thank you.
Best,
Claudio
--
C.
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