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[ESPResSo-users] Error when using mpirun


From: padidela uday
Subject: [ESPResSo-users] Error when using mpirun
Date: Tue, 29 Jul 2014 22:36:23 +0530

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?

Can any one help me to overcome this?


[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      


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