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Bug#712526: freefem++: FreeFem++-mpi not working
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Giuseppe Pitton
Jun 16, 2013, 4:00:02 PM6/16/13
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Package: freefem++
Version: 3.19.1-1
Severity: normal
Dear Maintainer,
I installed freefem++ on the default Wheezy (7.1) with apt-get, I also
installed freefem++-dev. I experienced the same issue on Wheezy (7.0).
FreeFem++ is working properly, but the parallel version FreeFem++-mpi does not.
I tried running the built-in examples of the examples++-mpi folder and they are
not working. The mentioned example files can be found at the following URL:
http://www.freefem.org/ff%2B%2B/ff%2B%2B/examples%2B%2B-mpi/
In particular, I tried running some test cases with both the following
commands:
FreeFem++-mpi chaleur3D-hips.edp
ff-mpirun -np 2 chaleur3D-mumps.edp
I obtain two kind of errors: msh3 libraries are missing or parallel solver
libraries are missing, for instance:
$ FreeFem++-mpi chaleur3D-pastix.edp
initparallele rank 0 on 1
-- FreeFem++ v 3.190001 (date Mer 9 mai 2012 21:50:21 CEST)
Load: lg_fem lg_mesh lg_mesh3 eigenvalue parallelempi
1 : // other
2 : load "msh3"
load error : msh3
fail :
list prefix: './' '/usr/lib/x86_64-linux-gnu/freefem++/' list suffix : '' ,
'.so'
Error line number 2, in file chaleur3D-pastix.edp, before token msh3
Error load
current line = 2 mpirank 0 / 1
Compile error : Error load
line number :2, msh3
error Compile error : Error load
line number :2, msh3
code = 1 mpirank: 0
FreeFem++-mpi finalize correctly .
$ FreeFem++-mpi chaleur3D-superludist.edp
initparallele rank 0 on 1
-- FreeFem++ v 3.190001 (date Mer 9 mai 2012 21:50:21 CEST)
Load: lg_fem lg_mesh lg_mesh3 eigenvalue parallelempi
1 : // other
2 : // NBPROC 2
3 : // ff-mpirun -np 4 chaleur3D-superludist.edp -glut ffglut -n 20 -op 1
-dt 0.01 -niter 10
4 :
5 : load "real_SuperLU_DIST_FreeFem"
load error : real_SuperLU_DIST_FreeFem
fail :
list prefix: './' '/usr/lib/x86_64-linux-gnu/freefem++/' list suffix : '' ,
'.so'
Error line number 5, in file chaleur3D-superludist.edp, before token
real_SuperLU_DIST_FreeFem
Error load
current line = 5 mpirank 0 / 1
Compile error : Error load
line number :5, real_SuperLU_DIST_FreeFem
error Compile error : Error load
line number :5, real_SuperLU_DIST_FreeFem
code = 1 mpirank: 0
FreeFem++-mpi finalize correctly .
I partially solved these issues compiling from source FreeFem++ v.3.23 with the
configure command:
../configure '--enable-download'
then make and make install as usual.
This however does not solve completely the problem since the make check gives
80 out of 84 test passed.
I have gcc 4.7.2 and openmpi 1.4.5.
I made HIPS, MUMPS and Super LU parallel solvers work, while HYPRE, pARMS and
pastix still do not. Here is one example of a working parallel simulation with
HIPS:
$ ff-mpirun -np 2 chaleur3D-hips.edp
'/opt/openmpi/1.6.4/bin/mpirun' -np 2 /usr/local/bin/FreeFem++-mpi chaleur3D-
hips.edp
initparallele rank 0 on 2
-- FreeFem++ v 3.230000 (date Sun Jun 16 19:29:19 CEST 2013)
Load: lg_fem lg_mesh lg_mesh3 eigenvalue parallelempi
(large output...)
~Hips_Solver S:0
times: compile 0.01s, execution 17.71s, mpirank:1
times: compile 0.01s, execution 18.46s, mpirank:0
######## We forget of deleting 3 Nb pointer, 0Bytes , mpirank 0
CodeAlloc : nb ptr 3401, size :382192 mpirank: 0
Bien: On a fini Normalement
######## We forget of deleting 3 Nb pointer, 0Bytes , mpirank 1
CodeAlloc : nb ptr 3401, size :382192 mpirank: 1
FreeFem++-mpi finalize correctly .
FreeFem++-mpi finalize correctly .
and an example of a failing simulation with HYPRE:
$ ff-mpirun -np 2 chaleur3D-hypre.edp
'/opt/openmpi/1.6.4/bin/mpirun' -np 2 /usr/local/bin/FreeFem++-mpi chaleur3D-
hypre.edp
initparallele rank 0 on 2
-- FreeFem++ v 3.230000 (date Sun Jun 16 19:29:19 CEST 2013)
Load: lg_fem lg_mesh lg_mesh3 eigenvalue parallelempi
1 :
current line = 5 mpirank 1 / 2
2 : // other
3 : load "msh3" (load: dlopen ../examples++-load/msh3.so 0x1416e60) load:
msh3
4 : load "medit" (load: dlopen ../examples++-load/medit.so 0x14187f0)
5 : load "hypre_FreeFem"
load error : hypre_FreeFem
fail :
list prefix: '../examples++-load/' '' './' list suffix : '' , '.so'
Error line number 5, in file chaleur3D-hypre.edp, before token hypre_FreeFem
Error load
current line = 5 mpirank 0 / 2
Compile error : Error load
line number :5, hypre_FreeFem
error Compile error : Error load
line number :5, hypre_FreeFem
code = 1 mpirank: 0
FreeFem++-mpi finalize correctly .
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
The other non-working solvers give the same error.
-- System Information:
Debian Release: 7.1
APT prefers stable
APT policy: (500, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 3.2.0-4-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages freefem++ depends on:
ii freeglut3 2.6.0-4
ii libamd2.2.0 1:3.4.0-3
ii libarpack2 3.1.1-2.1
ii libblas3 [libblas3gf] 1.2.20110419-5
ii libblas3gf 1.2.20110419-5
ii libc6 2.13-38
ii libgcc1 1:4.7.2-5
ii libgfortran3 4.7.2-5
ii libgl1-mesa-glx [libgl1] 8.0.5-4+deb7u1
ii libglu1-mesa [libglu1] 8.0.5-4+deb7u1
ii liblapack3 [liblapack3gf] 3.4.1+dfsg-1+deb70u1
ii libopenmpi1.3 1.4.5-1
ii libstdc++6 4.7.2-5
ii libumfpack5.4.0 1:3.4.0-3
ii libx11-6 2:1.5.0-1+deb7u1
ii libxext6 2:1.3.1-2+deb7u1
ii libxpm4 1:3.5.10-1
ii libxxf86vm1 1:1.1.2-1+deb7u1
freefem++ recommends no packages.
freefem++ suggests no packages.
--
To UNSUBSCRIBE, email to debian-bugs-...@lists.debian.org
with a subject of "unsubscribe". Trouble? Contact listm...@lists.debian.org
Version: 3.19.1-1
Severity: normal
Dear Maintainer,
I installed freefem++ on the default Wheezy (7.1) with apt-get, I also
installed freefem++-dev. I experienced the same issue on Wheezy (7.0).
FreeFem++ is working properly, but the parallel version FreeFem++-mpi does not.
I tried running the built-in examples of the examples++-mpi folder and they are
not working. The mentioned example files can be found at the following URL:
http://www.freefem.org/ff%2B%2B/ff%2B%2B/examples%2B%2B-mpi/
In particular, I tried running some test cases with both the following
commands:
FreeFem++-mpi chaleur3D-hips.edp
ff-mpirun -np 2 chaleur3D-mumps.edp
I obtain two kind of errors: msh3 libraries are missing or parallel solver
libraries are missing, for instance:
$ FreeFem++-mpi chaleur3D-pastix.edp
initparallele rank 0 on 1
-- FreeFem++ v 3.190001 (date Mer 9 mai 2012 21:50:21 CEST)
Load: lg_fem lg_mesh lg_mesh3 eigenvalue parallelempi
1 : // other
2 : load "msh3"
load error : msh3
fail :
list prefix: './' '/usr/lib/x86_64-linux-gnu/freefem++/' list suffix : '' ,
'.so'
Error line number 2, in file chaleur3D-pastix.edp, before token msh3
Error load
current line = 2 mpirank 0 / 1
Compile error : Error load
line number :2, msh3
error Compile error : Error load
line number :2, msh3
code = 1 mpirank: 0
FreeFem++-mpi finalize correctly .
$ FreeFem++-mpi chaleur3D-superludist.edp
initparallele rank 0 on 1
-- FreeFem++ v 3.190001 (date Mer 9 mai 2012 21:50:21 CEST)
Load: lg_fem lg_mesh lg_mesh3 eigenvalue parallelempi
1 : // other
2 : // NBPROC 2
3 : // ff-mpirun -np 4 chaleur3D-superludist.edp -glut ffglut -n 20 -op 1
-dt 0.01 -niter 10
4 :
5 : load "real_SuperLU_DIST_FreeFem"
load error : real_SuperLU_DIST_FreeFem
fail :
list prefix: './' '/usr/lib/x86_64-linux-gnu/freefem++/' list suffix : '' ,
'.so'
Error line number 5, in file chaleur3D-superludist.edp, before token
real_SuperLU_DIST_FreeFem
Error load
current line = 5 mpirank 0 / 1
Compile error : Error load
line number :5, real_SuperLU_DIST_FreeFem
error Compile error : Error load
line number :5, real_SuperLU_DIST_FreeFem
code = 1 mpirank: 0
FreeFem++-mpi finalize correctly .
I partially solved these issues compiling from source FreeFem++ v.3.23 with the
configure command:
../configure '--enable-download'
then make and make install as usual.
This however does not solve completely the problem since the make check gives
80 out of 84 test passed.
I have gcc 4.7.2 and openmpi 1.4.5.
I made HIPS, MUMPS and Super LU parallel solvers work, while HYPRE, pARMS and
pastix still do not. Here is one example of a working parallel simulation with
HIPS:
$ ff-mpirun -np 2 chaleur3D-hips.edp
'/opt/openmpi/1.6.4/bin/mpirun' -np 2 /usr/local/bin/FreeFem++-mpi chaleur3D-
hips.edp
initparallele rank 0 on 2
-- FreeFem++ v 3.230000 (date Sun Jun 16 19:29:19 CEST 2013)
Load: lg_fem lg_mesh lg_mesh3 eigenvalue parallelempi
(large output...)
~Hips_Solver S:0
times: compile 0.01s, execution 17.71s, mpirank:1
times: compile 0.01s, execution 18.46s, mpirank:0
######## We forget of deleting 3 Nb pointer, 0Bytes , mpirank 0
CodeAlloc : nb ptr 3401, size :382192 mpirank: 0
Bien: On a fini Normalement
######## We forget of deleting 3 Nb pointer, 0Bytes , mpirank 1
CodeAlloc : nb ptr 3401, size :382192 mpirank: 1
FreeFem++-mpi finalize correctly .
FreeFem++-mpi finalize correctly .
and an example of a failing simulation with HYPRE:
$ ff-mpirun -np 2 chaleur3D-hypre.edp
'/opt/openmpi/1.6.4/bin/mpirun' -np 2 /usr/local/bin/FreeFem++-mpi chaleur3D-
hypre.edp
initparallele rank 0 on 2
-- FreeFem++ v 3.230000 (date Sun Jun 16 19:29:19 CEST 2013)
Load: lg_fem lg_mesh lg_mesh3 eigenvalue parallelempi
1 :
current line = 5 mpirank 1 / 2
2 : // other
3 : load "msh3" (load: dlopen ../examples++-load/msh3.so 0x1416e60) load:
msh3
4 : load "medit" (load: dlopen ../examples++-load/medit.so 0x14187f0)
5 : load "hypre_FreeFem"
load error : hypre_FreeFem
fail :
list prefix: '../examples++-load/' '' './' list suffix : '' , '.so'
Error line number 5, in file chaleur3D-hypre.edp, before token hypre_FreeFem
Error load
current line = 5 mpirank 0 / 2
Compile error : Error load
line number :5, hypre_FreeFem
error Compile error : Error load
line number :5, hypre_FreeFem
code = 1 mpirank: 0
FreeFem++-mpi finalize correctly .
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
The other non-working solvers give the same error.
-- System Information:
Debian Release: 7.1
APT prefers stable
APT policy: (500, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 3.2.0-4-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages freefem++ depends on:
ii freeglut3 2.6.0-4
ii libamd2.2.0 1:3.4.0-3
ii libarpack2 3.1.1-2.1
ii libblas3 [libblas3gf] 1.2.20110419-5
ii libblas3gf 1.2.20110419-5
ii libc6 2.13-38
ii libgcc1 1:4.7.2-5
ii libgfortran3 4.7.2-5
ii libgl1-mesa-glx [libgl1] 8.0.5-4+deb7u1
ii libglu1-mesa [libglu1] 8.0.5-4+deb7u1
ii liblapack3 [liblapack3gf] 3.4.1+dfsg-1+deb70u1
ii libopenmpi1.3 1.4.5-1
ii libstdc++6 4.7.2-5
ii libumfpack5.4.0 1:3.4.0-3
ii libx11-6 2:1.5.0-1+deb7u1
ii libxext6 2:1.3.1-2+deb7u1
ii libxpm4 1:3.5.10-1
ii libxxf86vm1 1:1.1.2-1+deb7u1
freefem++ recommends no packages.
freefem++ suggests no packages.
--
To UNSUBSCRIBE, email to debian-bugs-...@lists.debian.org
with a subject of "unsubscribe". Trouble? Contact listm...@lists.debian.org
Dimitrios Eftaxiopoulos
Jun 17, 2013, 6:40:02 AM6/17/13
to
Hello Giuseppe
Thank you for raising the mpi related issues.
The failing to load msh3 seems to me to be a more general issue not related to
the parallel solver in particular.
For the rest of the problems I do not have an immediate answer.
I plan to try to upload freefem++-3.23 to unstable shortly so I will have a
look on these issues.
Best regards
Dimitris
Thank you for raising the mpi related issues.
The failing to load msh3 seems to me to be a more general issue not related to
the parallel solver in particular.
For the rest of the problems I do not have an immediate answer.
I plan to try to upload freefem++-3.23 to unstable shortly so I will have a
look on these issues.
Best regards
Dimitris
Giuseppe Pitton
Jun 18, 2013, 7:10:02 AM6/18/13
to
Dear Dimitris,
here are some thoughts on how to solve the issue (i tried to make HYPRE solver work).
Installing from source FreeFem++-3.23 I noticed that in the folder ff++/downloads/hypre nothing was built. So I compiled manually hypre-2.9.0b from source and I changed the paths in the file ff++/src/solver/makefile-sparsesolver.inc and I also commented the non HYPRE lines in ff++/src/solver/makefile. Please note that I had to modify several other lines in ff++/src/solver/makefile-sparsesolver.inc, in particular:
on line 56 after MPI_INCLUDE = there is a /I/ that should instead be a -I
on line 77 suffix should be changed to so
several paths should be adapted to the system in use (for instance lines 87, 121, 126, 130, 135 and of course lines 185 and following)
lines 99 and 100 should be commented
then moving in directory ff++/src/solver and running make I get a hypre_FreeFem.so that I moved to FreeFem++ library directory (/usr/local/lib/ff++/3.23/lib/ on my system). Now HYPRE is running but not working, see this test case for instance:
$ ff-mpirun -np 2 chaleur3d-hypre.edp
-- Square mesh : nb vertices =441 , nb triangles = 800 , nb boundary edges 80
-- Square mesh : nb vertices =441 , nb triangles = 800 , nb boundary edges 80
-- Build Nodes/DF on mesh : n.v. 9261, n. elmt. 48000, n b. elmt. 4800
nb of Nodes 68921 nb of DoF 68921 DFon=1100
-- FESpace: Nb of Nodes 68921 Nb of DoF 68921
-- Build Nodes/DF on mesh : n.v. 9261, n. elmt. 48000, n b. elmt. 4800
nb of Nodes 68921 nb of DoF 68921 DFon=1100
-- FESpace: Nb of Nodes 68921 Nb of DoF 68921
###########DEFAULT PARAMETERS WILL BE SET#######
SOLVER: AMG-GMRES
tgv1e+10
time 0.01
tgv1e+10
time 0.01
*** Process received signal ***
Signal: Segmentation fault: 11 (11)
Signal code: Address not mapped (1)
Failing at address: 0x7f88d259d880
*** Process received signal ***
Signal: Segmentation fault: 11 (11)
Signal code: Address not mapped (1)
Failing at address: 0x7fe9f2d9d5c0
*** End of error message ***
*** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 550 on node (...) exited on signal 11 (Segmentation fault: 11).
--------------------------------------------------------------------------
Hope this helps.
Best regards.
Giuseppe
here are some thoughts on how to solve the issue (i tried to make HYPRE solver work).
Installing from source FreeFem++-3.23 I noticed that in the folder ff++/downloads/hypre nothing was built. So I compiled manually hypre-2.9.0b from source and I changed the paths in the file ff++/src/solver/makefile-sparsesolver.inc and I also commented the non HYPRE lines in ff++/src/solver/makefile. Please note that I had to modify several other lines in ff++/src/solver/makefile-sparsesolver.inc, in particular:
on line 56 after MPI_INCLUDE = there is a /I/ that should instead be a -I
on line 77 suffix should be changed to so
several paths should be adapted to the system in use (for instance lines 87, 121, 126, 130, 135 and of course lines 185 and following)
lines 99 and 100 should be commented
then moving in directory ff++/src/solver and running make I get a hypre_FreeFem.so that I moved to FreeFem++ library directory (/usr/local/lib/ff++/3.23/lib/ on my system). Now HYPRE is running but not working, see this test case for instance:
$ ff-mpirun -np 2 chaleur3d-hypre.edp
initparallele rank 0 on 2
-- FreeFem++ v 3.230000 (date Jeu 6 jui 2013 20:58:44 CEST)
Load: lg_fem lg_mesh lg_mesh3 eigenvalue parallelempi
(large output)
-- Square mesh : nb vertices =441 , nb triangles = 800 , nb boundary edges 80
-- Square mesh : nb vertices =441 , nb triangles = 800 , nb boundary edges 80
-- Build Nodes/DF on mesh : n.v. 9261, n. elmt. 48000, n b. elmt. 4800
nb of Nodes 68921 nb of DoF 68921 DFon=1100
-- FESpace: Nb of Nodes 68921 Nb of DoF 68921
-- Build Nodes/DF on mesh : n.v. 9261, n. elmt. 48000, n b. elmt. 4800
nb of Nodes 68921 nb of DoF 68921 DFon=1100
-- FESpace: Nb of Nodes 68921 Nb of DoF 68921
###########DEFAULT PARAMETERS WILL BE SET#######
SOLVER: AMG-GMRES
tgv1e+10
time 0.01
tgv1e+10
time 0.01
*** Process received signal ***
Signal: Segmentation fault: 11 (11)
Signal code: Address not mapped (1)
Failing at address: 0x7f88d259d880
*** Process received signal ***
Signal: Segmentation fault: 11 (11)
Signal code: Address not mapped (1)
Failing at address: 0x7fe9f2d9d5c0
*** End of error message ***
*** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 550 on node (...) exited on signal 11 (Segmentation fault: 11).
--------------------------------------------------------------------------
Hope this helps.
Best regards.
Giuseppe
Giuseppe Pitton
Aug 23, 2013, 8:50:02 AM8/23/13
to
Dear Dimitrios,
from the FreeFem++ mailing list:
we know now that Hypre was disabled by the developers for some reason. Now, from v. 3.25 it is possible to configure with the option "--enable-hypre" which correctly builds the hypre_FreeFem.so file. It worked for me.
Kind regards.
Giuseppe
Dimitrios Eftaxiopoulos
Aug 24, 2013, 3:50:02 AM8/24/13
to
Hello Giuseppe,
Thanks for the info. I have subscribed to the FreeFem++ mailing list and I
have read the relevant thread. I will try to implement this option when
version 3.25 will be packaged.
In the mean time I will upload v. 3.23 in 1-2 weeks. The failing of "load
msh3" is fixed. Also, by running dh_auto_test from the debian/rules file after
the package build, which tries to compile all the example .edp files, I noticed
that several of them (not all) in the examples++-mpi folder run successfully.
So I presume that we have a partially working FreeFem++-mpi command.
Best regards
Dimitris
Thanks for the info. I have subscribed to the FreeFem++ mailing list and I
have read the relevant thread. I will try to implement this option when
version 3.25 will be packaged.
In the mean time I will upload v. 3.23 in 1-2 weeks. The failing of "load
msh3" is fixed. Also, by running dh_auto_test from the debian/rules file after
the package build, which tries to compile all the example .edp files, I noticed
that several of them (not all) in the examples++-mpi folder run successfully.
So I presume that we have a partially working FreeFem++-mpi command.
Best regards
Dimitris
Alya
Dec 18, 2021, 1:20:03 PM12/18/21
to
--
I miei umili saluti
Mio buon amico, come stai, ho un fondo di beneficenza che donerò con
il tuo aiuto. Prova a contattarmi per maggiori informazioni. Ti dirò
di più su di me e sui miei piani con questi soldi quando avrò tue
notizie.
Aspetto una tua risposta per darti maggiori dettagli.
----------------------------
my humble regards,
Dear friend how are you, I have a charitable donation fund that I want
to donate by helping you. Please try to get back to me for more
information. I will tell you more about myself and my plans with this
money when I hear from you.
Awaiting your reply to give me more details.
I miei umili saluti
Mio buon amico, come stai, ho un fondo di beneficenza che donerò con
il tuo aiuto. Prova a contattarmi per maggiori informazioni. Ti dirò
di più su di me e sui miei piani con questi soldi quando avrò tue
notizie.
Aspetto una tua risposta per darti maggiori dettagli.
----------------------------
my humble regards,
Dear friend how are you, I have a charitable donation fund that I want
to donate by helping you. Please try to get back to me for more
information. I will tell you more about myself and my plans with this
money when I hear from you.
Awaiting your reply to give me more details.
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