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Re: [ESPResSo-users] Error when using mpirun


From: Axel Arnold
Subject: Re: [ESPResSo-users] Error when using mpirun
Date: Wed, 30 Jul 2014 09:57:04 +0200
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Thunderbird/24.6.0

On 07/29/2014 07:06 PM, padidela uday wrote:
Hello everyone

Can anyone help me how to overcome this error?
When I tried to run my script using mpi this error has been shown on the terminal.
I think its the problem with threading?


No, the problem is with OpenMPI, as it seems. This might be a bad interaction between your OpenMPI and FFTW, but can also just be a bad OpenMPI configuration, according to what google finds.

Can any one help me to overcome this?

No, that requires some deeper debugging on your specific system. You can try to use a newer OpenMPI or a different MPI library.

Axel


[bits-goa:03511] *** Process received signal ***
[bits-goa:03511] Signal: Bus error (7)
[bits-goa:03511] Signal code: Non-existant physical address (2)
[bits-goa:03511] Failing at address: 0x7f7b6a2c9000
[bits-goa:03513] *** Process received signal ***
[bits-goa:03513] Signal: Bus error (7)
[bits-goa:03513] Signal code: Non-existant physical address (2)
[bits-goa:03513] Failing at address: 0x7fb0374af000
[bits-goa:03513] [ 0] /lib64/libpthread.so.0() [0x3280c0f710]
[bits-goa:03513] [ 1] ./Espresso(__intel_ssse3_rep_memcpy+0x19df) [0x626edf]
[bits-goa:03513] [ 2] /opt/opmi/1.6.4/lib/libmpi.so.1(opal_convertor_pack+0x101) [0x7fb040d77ad1]
[bits-goa:03513] [ 3] /opt/opmi/1.6.4/lib/openmpi/mca_btl_sm.so(mca_btl_sm_prepare_src+0xfc) [0x7fb03c8856fc]
[bits-goa:03513] [ 4] /opt/opmi/1.6.4/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_request_schedule_once+0x194) [0x7fb03d0aac64]
[bits-goa:03513] [ 5] /opt/opmi/1.6.4/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_recv_frag_callback_ack+0x316) [0x7fb03d0a1c36]
[bits-goa:03513] [ 6] /opt/opmi/1.6.4/lib/openmpi/mca_btl_sm.so(mca_btl_sm_component_progress+0x2cd) [0x7fb03c886d5d]
[bits-goa:03513] [ 7] /opt/opmi/1.6.4/lib/libmpi.so.1(opal_progress+0xa9) [0x7fb040d83b39]
[bits-goa:03513] [ 8] /opt/opmi/1.6.4/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send+0x582) [0x7fb03d09e122]
[bits-goa:03513] [ 9] /opt/opmi/1.6.4/lib/libmpi.so.1(MPI_Send+0x5d) [0x7fb040cd561d]
[bits-goa:03513] [10] ./Espresso(fft_perform_forw+0x422) [0x507aa2]
[bits-goa:03513] [11] ./Espresso(p3m_calc_kspace_forces+0x2e4) [0x4b1da4]
[bits-goa:03513] [12] ./Espresso(force_calc+0xff) [0x50b4ef]
[bits-goa:03513] [13] ./Espresso(integrate_vv+0x56) [0x432d46]
[bits-goa:03513] [14] ./Espresso(mpi_integrate_slave+0x8) [0x41b948]
[bits-goa:03513] [15] ./Espresso(mpi_loop+0x57) [0x420017]
[bits-goa:03513] [16] ./Espresso(main+0x80) [0x419af0]
[bits-goa:03513] [17] /lib64/libc.so.6(__libc_start_main+0xfd) [0x328001ed1d]
[bits-goa:03513] [18] ./Espresso() [0x419999]
[bits-goa:03513] *** End of error message ***
[bits-goa:03511] [ 0] /lib64/libpthread.so.0() [0x3280c0f710]
[bits-goa:03511] [ 1] ./Espresso(__intel_ssse3_rep_memcpy+0x19df) [0x626edf]
[bits-goa:03511] [ 2] /opt/opmi/1.6.4/lib/libmpi.so.1(opal_convertor_pack+0x101) [0x7f7b73b19ad1]
[bits-goa:03511] [ 3] /opt/opmi/1.6.4/lib/openmpi/mca_btl_sm.so(mca_btl_sm_prepare_src+0xfc) [0x7f7b6f6276fc]
[bits-goa:03511] [ 4] /opt/opmi/1.6.4/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_request_schedule_once+0x194) [0x7f7b6fe4cc64]
[bits-goa:03511] [ 5] /opt/opmi/1.6.4/lib/openmpi/mca_pml_ob1.so(+0x11168) [0x7f7b6fe4a168]
[bits-goa:03511] [ 6] /opt/opmi/1.6.4/lib/openmpi/mca_btl_sm.so(mca_btl_sm_component_progress+0x60e) [0x7f7b6f62909e]
[bits-goa:03511] [ 7] /opt/opmi/1.6.4/lib/libmpi.so.1(opal_progress+0xa9) [0x7f7b73b25b39]
[bits-goa:03511] [ 8] /opt/opmi/1.6.4/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send+0x582) [0x7f7b6fe40122]
[bits-goa:03511] [ 9] /opt/opmi/1.6.4/lib/libmpi.so.1(MPI_Send+0x5d) [0x7f7b73a7761d]
[bits-goa:03511] [10] ./Espresso(fft_perform_forw+0x422) [0x507aa2]
[bits-goa:03511] [11] ./Espresso(p3m_calc_kspace_forces+0x2e4) [0x4b1da4]
[bits-goa:03511] [12] ./Espresso(force_calc+0xff) [0x50b4ef]
[bits-goa:03511] [13] ./Espresso(integrate_vv+0x56) [0x432d46]
[bits-goa:03511] [14] ./Espresso(mpi_integrate+0x8e) [0x41b8fe]
[bits-goa:03511] [15] ./Espresso(time_force_calc+0x1c) [0x47b8ec]
[bits-goa:03511] [16] ./Espresso() [0x4b64cc]
[bits-goa:03511] [17] ./Espresso(p3m_adaptive_tune+0x820) [0x4b3710]
[bits-goa:03511] [18] ./Espresso(tclcommand_inter_coulomb_parse_p3m_tune+0x499) [0x4f2279]
[bits-goa:03511] [19] ./Espresso(tclcommand_inter_coulomb_parse_p3m+0x273) [0x4f1ce3]
[bits-goa:03511] [20] ./Espresso(tclcommand_inter_parse_coulomb+0x454) [0x4c2b54]
[bits-goa:03511] [21] ./Espresso(tclcommand_inter+0xf61) [0x4c20a1]
[bits-goa:03511] [22] /usr/local/lib/libtcl8.6.so(TclInvokeStringCommand+0x7f) [0x7f7b73e2a85f]
[bits-goa:03511] [23] /usr/local/lib/libtcl8.6.so(TclNREvalObjv+0x66d) [0x7f7b73e2c32d]
[bits-goa:03511] [24] /usr/local/lib/libtcl8.6.so(Tcl_EvalObjv+0x24) [0x7f7b73e2c564]
[bits-goa:03511] [25] /usr/local/lib/libtcl8.6.so(+0x3af6d) [0x7f7b73e2cf6d]
[bits-goa:03511] [26] /usr/local/lib/libtcl8.6.so(Tcl_FSEvalFileEx+0x236) [0x7f7b73ec87c6]
[bits-goa:03511] [27] /usr/local/lib/libtcl8.6.so(Tcl_MainEx+0x2fe) [0x7f7b73eceace]
[bits-goa:03511] [28] ./Espresso(main+0x77) [0x419ae7]
[bits-goa:03511] [29] /lib64/libc.so.6(__libc_start_main+0xfd) [0x328001ed1d]
[bits-goa:03511] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 3513 on node bits-goa exited on signal 7 (Bus error).
--------------------------------------------------------------------------
2 total processes killed (some possibly by mpirun during cleanup)

Thank you

With Kind Regards

Uday      



-- 
JP Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609

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