Hi All,
I got the following error message during relion autopicking, does anybody have suggestions?
Thanks,
Xinchao
*-----------------------------WARNING------------------------------------------------*
With the current settings the GPU memory is imposing a soft limit on your performace,
since one or more micrographs has to use (at least 3) batches of orientations to-----*
achieve the total requested 72 orientations. Consider using
*--------higher --ang---------WARNING------------------------------------------------*
With the harder --shrinks the GPU memory is imposing a soft limit on your performace,
since onehigher --lowpass with --shrink 0(at least 3) batches of orientations to
*------------------------------------------------------------------------------------*
higher --ang
*-----------------------------WARNING------------------------------------------------*
With the current settings the GPU memory is imposing a soft limit on your performace,
since one or more micrographs has to use (at least 3) batches of orientations to-----*
achieve the total requested 72 orientations. Consider using
*--------higher --ang---------WARNING------------------------------------------------*
With the harder --shrinks the GPU memory is imposing a soft limit on your performace,
since onehigher --lowpass with --shrink 0(at least 3) batches of orientations to
*------------------------------------------------------------------------------------*
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
[ussf-papp-gpu02:31066] *** Process received signal ***
[ussf-papp-gpu02:31066] Signal: Aborted (6)------------------------------------------*
[ussf-papp-gpu02:31066] Signal code: (-6)
[ussf-papp-gpu02:31066] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x2b2a1f7e95e0]---------*
[ussf-papp-gpu02:31066] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b2a2066b1f7]erformace,
[ussf-papp-gpu02:31066] [ 2] /lib64/libc.so.6(abort+0x148)[0x2b2a2066c8e8]ons to
[ussf-papp-gpu02:31066] [ 3] /lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x165)[0x2b2a1fc5e9d5]
[ussf-papp-gpu02:31066] [ 4] /lib64/libstdc++.so.6(+0x5e946)[0x2b2a1fc5c946]
[ussf-papp-gpu02:31066] [ 5] /lib64/libstdc++.so.6(+0x5e973)[0x2b2a1fc5c973]
[ussf-papp-gpu02:31066] [ 6] /lib64/libstdc++.so.6(+0x5eb93)[0x2b2a1fc5cb93]
[ussf-papp-gpu02:31066] [ 7] /lib64/libstdc++.so.6(+0xb3652)[0x2b2a1fcb1652]---------*
[ussf-papp-gpu02:31066] [ 8] /common/cryoem/RHEL7/relion3-beta/bin/relion_autopick_mpi(_ZN13MetaDataTable15columnHistogramE8EMDLabelRSt6vectorIdSaIdEES4_iP7CPlot2Dlddbb+0x1134)[0x5013a4]--------------------------WARNING------------------------------------------------*
[ussf-papp-gpu02:31066] [ 9] /common/cryoem/RHEL7/relion3-beta/bin/relion_autopick_mpi(_ZN10AutoPicker18generatePDFLogfileEv+0xc55)[0x43d505]
[ussf-papp-gpu02:31066] [10] /common/cryoem/RHEL7/relion3-beta/bin/relion_autopick_mpi(main+0x13f)[0x42d70f]
[ussf-papp-gpu02:31066] [11] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b2a20657c05]
[ussf-papp-gpu02:31066] [12] /common/cryoem/RHEL7/relion3-beta/bin/relion_autopick_mpi[0x430aff]
[ussf-papp-gpu02:31066] *** End of error message ***
[warn] Epoll ADD(4) on fd 39 failed. Old events were 0; read change was 0 (none); write change was 1 (add): Bad file descriptor
[warn] Epoll ADD(4) on fd 52 failed. Old events were 0; read change was 0 (none); write change was 1 (add): Bad file descriptor
[warn] Epoll ADD(4) on fd 36 failed. Old events were 0; read change was 0 (none); write change was 1 (add): Bad file descriptor
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