Subject: [FEniCS-users] dolfin openmpi

From: Patrick Riesen <[email-masked]>
Date: Wed, 7 Oct 2009 17:39:05 +0200

hi, i catched up with dolfin 0.9.3 on my linux workstation. install & 
compile went fine and running demos in serial seems to be ok as well.
i was trying to run the demos in parallel but i get errors with openmpi 
as follows:
(this occured running any dem with mpirun -np xy ./demo where xy is 
larger than 1, it did not occur for -np 1):

------------
{process output.....}

then suddenly

[vierzack01:12050] *** An error occurred in MPI_Barrier
[vierzack01:12049] *** An error occurred in MPI_Barrier
[vierzack01:12049] *** on communicator MPI_COMM_WORLD
[vierzack01:12049] *** MPI_ERR_COMM: invalid communicator
[vierzack01:12049] *** MPI_ERRORS_ARE_FATAL (goodbye)
[vierzack01:12050] *** on communicator MPI_COMM_WORLD
[vierzack01:12050] *** MPI_ERR_COMM: invalid communicator
[vierzack01:12050] *** MPI_ERRORS_ARE_FATAL (goodbye)
[vierzack01:12049] *** Process received signal ***
[vierzack01:12049] Signal: Segmentation fault (11)
[vierzack01:12049] Signal code: Address not mapped (1)
[vierzack01:12049] Failing at address: 0x4
[vierzack01:12050] *** Process received signal ***
[vierzack01:12050] Signal: Segmentation fault (11)
[vierzack01:12050] Signal code: Address not mapped (1)
[vierzack01:12050] Failing at address: 0x4
[vierzack01:12049] [ 0] /lib/libpthread.so.0 [0x7f0fd3be6410]
[vierzack01:12049] [ 1] 
/home/priesen/num/openmpi/lib/libopen-rte.so.0(orte_smr_base_set_proc_state+0x34) 
[0x7f0fd475c1d4]
[vierzack01:12049] [ 2] 
/home/priesen/num/openmpi/lib/libmpi.so.0(ompi_mpi_finalize+0x11b) 
[0x7f0fd48a8b0b]
[vierzack01:12049] [ 3] 
/scratch-second/priesen/FEniCS/build/lib/libdolfin.so.0(_ZN6dolfin17SubSystemsManager12finalize_mpiEv+0x35) 
[0x7f0fd7bbfb15]
[vierzack01:12049] [ 4] 
/scratch-second/priesen/FEniCS/build/lib/libdolfin.so.0(_ZN6dolfin17SubSystemsManagerD1Ev+0xe) 
[0x7f0fd7bbfb2e]
[vierzack01:12049] [ 5] /lib/libc.so.6(__cxa_finalize+0x6c) [0x7f0fd39cee0c]
[vierzack01:12049] [ 6] 
/scratch-second/priesen/FEniCS/build/lib/libdolfin.so.0 [0x7f0fd7aa65d3]
[vierzack01:12049] *** End of error message ***
[vierzack01:12050] [ 0] /lib/libpthread.so.0 [0x7fd707916410]
[vierzack01:12050] [ 1] 
/home/priesen/num/openmpi/lib/libopen-rte.so.0(orte_smr_base_set_proc_state+0x34) 
[0x7fd70848c1d4]
[vierzack01:12050] [ 2] 
/home/priesen/num/openmpi/lib/libmpi.so.0(ompi_mpi_finalize+0x11b) 
[0x7fd7085d8b0b]
[vierzack01:12050] [ 3] 
/scratch-second/priesen/FEniCS/build/lib/libdolfin.so.0(_ZN6dolfin17SubSystemsManager12finalize_mpiEv+0x35) 
[0x7fd70b8efb15]
[vierzack01:12050] [ 4] 
/scratch-second/priesen/FEniCS/build/lib/libdolfin.so.0(_ZN6dolfin17SubSystemsManagerD1Ev+0xe) 
[0x7fd70b8efb2e]
[vierzack01:12050] [ 5] /lib/libc.so.6(__cxa_finalize+0x6c) [0x7fd7076fee0c]
[vierzack01:12050] [ 6] 
/scratch-second/priesen/FEniCS/build/lib/libdolfin.so.0 [0x7fd70b7d65d3]
[vierzack01:12050] *** End of error message ***
mpirun noticed that job rank 0 with PID 12049 on node vierzack01 exited 
on signal 15 (Terminated).
1 additional process aborted (not shown)
------------

Is this a openmpi error?
Is there a specific version of openmpi required for dolfin?
mine is 1.2.8 and it worked up to dolfin 0.9.2

best,
patrick

---

From: Anders Logg <[email-masked]>
Date: Wed, 7 Oct 2009 22:24:21 +0200

> larger than 1, it did not occur for -np 1):

No idea what goes wrong. My version of OpenMPI is 1.3.2-3ubuntu1.

DOLFIN wasn't parallel before 0.9.3 so I'm not sure what you mean by
it working up to 0.9.2.

--
Anders