Bug#712526: Re: Bug#712526: freefem++: FreeFem++-mpi not working
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 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 signature.asc Description: This is a digitally signed message part.
Bug#712526: freefem++: FreeFem++-mpi not working
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 3.23 (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 68921nb 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 68921nb 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
Bug#712526: freefem++: FreeFem++-mpi not working
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 3.23 (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 68921nb 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 68921nb 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
Bug#712526: freefem++: FreeFem++-mpi not working
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 3.23 (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 3.23 (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
Bug#712526: freefem++: FreeFem++-mpi not working
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 3.23 (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 3.23 (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:
