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Subject: [OMPI users] crash with hardware virtualization
From: Philippe Gouret (philippe.gouret_at_[hidden])
Date: 2011-10-13 04:33:40


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