Bug#712526: freefem++: FreeFem++-mpi not working
Giuseppe Pitton
giuseppe.pitton at gmail.com
Fri Aug 23 12:43:22 UTC 2013
Dear Dimitrios,
from the FreeFem++ mailing list:
http://ljll.math.upmc.fr/pipermail/freefempp/2013-July/002839.html
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
Il giorno 18/giu/2013, alle ore 12:57, Giuseppe Pitton ha scritto:
> 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
> 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
>
>
> Il giorno 17/giu/2013, alle ore 12:18, Dimitrios Eftaxiopoulos ha scritto:
>
>> 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
>>
>> On Sunday 16 of June 2013 21:47:49 you wrote:
>>> 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.
>
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