Hi everyone I use OpenMPI on single a multi-cores computer to benefit of parralel computing with bioinformatics tools like: tree-ppuzzle ... (computation tools using MPI standard).
Workstation's caracteristics: AMD, 64-bits, 2 processors, 4 cores by processors, Ubuntu 64 bits AMD-V hardware virtualization technology is activated The command "mpirun -np 8 tree-ppuzzle data_file" works perfectly and produces the expected results. I would like to be able to do the same things on VirtualBox VMs. To produce some tests, i created an Ubuntu (11.04) 64 bits VM with Virtualbox, i installed OpenMPI 1.4.3 and tree-ppuzzle 5.2. When i run the same command: "mpirun -np 8 tree-ppuzzle data_file", it crashes after few seconds. The error message is: [philippe-VirtualBox:01542] Signal: Segmentation fault (11) [philippe-VirtualBox:01542] Signal code: Address not mapped (1) [philippe-VirtualBox:01542] Failing at address: (nil) [philippe-VirtualBox:01541] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfc60) [0x7f5b23fb4c60] [philippe-VirtualBox:01541] [ 1] /usr/lib/libsprng.so.2(get_rn_dbl+0x4) [0x7f5b251c3d20] [philippe-VirtualBox:01542] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfc60) [0x7fb9de606c60] [philippe-VirtualBox:01542] [ 1] /usr/lib/libsprng.so.2(get_rn_dbl+0x4) [0x7fb9df815d20] [philippe-VirtualBox:01542] [ 2] tree-ppuzzle(randominteger+0xf) [0x4347ef] [philippe-VirtualBox:01542] [ 3] tree-ppuzzle(chooser+0x4a) [0x43513a] [philippe-VirtualBox:01542] [ 4] tree-ppuzzle(allpstep+0x8c) [0x432f2c] [philippe-VirtualBox:01542] [ 5] tree-ppuzzle(slave_main+0x539) [0x43f119] [philippe-VirtualBox:01542] [ 6] tree-ppuzzle(main+0x67e) [0x42e84e] [philippe-VirtualBox:01542] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff) [0x7fb9de281eff] [philippe-VirtualBox:01542] [ 8] tree-ppuzzle() [0x4099d9] [philippe-VirtualBox:01542] *** End of error message *** [philippe-VirtualBox:01541] [ 2] tree-ppuzzle(randominteger+0xf) [0x4347ef] [philippe-VirtualBox:01541] [ 3] tree-ppuzzle(chooser+0x4a) [0x43513a] [philippe-VirtualBox:01541] [ 4] tree-ppuzzle(allpstep+0x8c) [0x432f2c] [philippe-VirtualBox:01541] [ 5] tree-ppuzzle(slave_main+0x539) [0x43f119] [philippe-VirtualBox:01541] [ 6] tree-ppuzzle(main+0x67e) [0x42e84e] [philippe-VirtualBox:01541] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff) [0x7f5b23c2feff] [philippe-VirtualBox:01541] [ 8] tree-ppuzzle() [0x4099d9] [philippe-VirtualBox:01541] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 7 with PID 1542 on node philippe-VirtualBox exited on signal 11 (Segmentation fault). If i disable AMD-V virtualization, all works perfectly. I join the data_file to this email. can you help me ? Thanks by advance Best regards Philippe Gouret EBM Laboratory - UMR 6632 University of Provence Marseille - France
test_tp3.alig
Description: File Attachment: test_tp3.alig
