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Hi,

I am having some issues with relion_refine_mpi. I am using relion v2.0.5 in
a machine running Ubuntu 14.04 with CUDA 8.0 and openmpi-2.0.2. I can run
gctf using MPI, but I get an error when I try to run a 2D or 3D
classification.

if I run:

*mpirun -n 5 `which relion_refine_mpi` --o Class2D/job022/run --i
./Extract/job008/particles.star --dont_combine_weights_via_disc
--no_parallel_disc_io --preread_images  --pool 10 --ctf  --iter 25
--tau2_fudge 2 --particle_diameter 220 --K 50 --flatten_solvent
--zero_mask  --oversampling 1 --psi_step 12 --offset_range 5 --offset_step
2 --norm --scale  --j 1 --gpu ""*

I get this error message:





























































*  1: MPI_ERR_TYPE: invalid datatype  1: MPI_ERR_TYPE: invalid datatype  2:
MPI_ERR_TYPE: invalid datatype  2: MPI_ERR_TYPE: invalid datatype  3:
MPI_ERR_TYPE: invalid datatype  3: MPI_ERR_TYPE: invalid datatype  4:
MPI_ERR_TYPE: invalid datatype  4: MPI_ERR_TYPE: invalid datatypeterminate
called after throwing an instance of 'RelionError'terminate called after
throwing an instance of 'RelionError'[ubuntu:05596] *** Process received
signal ***terminate called after throwing an instance of
'RelionError'[ubuntu:05597] *** Process received signal ***[ubuntu:05598]
*** Process received signal ***[ubuntu:05598] Signal: Aborted
(6)[ubuntu:05598] Signal code:  (-6)[ubuntu:05597] Signal: Aborted
(6)[ubuntu:05597] Signal code:  (-6)[ubuntu:05596] Signal: Aborted
(6)[ubuntu:05596] Signal code:  (-6)[ubuntu:05596] [ 0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x10330)[0x7fe484847330][ubuntu:05596]
[ 1] [ubuntu:05598] [ 0] [ubuntu:05597] [ 0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x10330)[0x7f622e526330][ubuntu:05597]
[ 1]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)[0x7fe4844a8c37][ubuntu:05596]
[ 2]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x10330)[0x7f7fd2524330][ubuntu:05598]
[ 1]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)[0x7f622e187c37][ubuntu:05597]
[ 2]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x148)[0x7fe4844ac028][ubuntu:05596]
[ 3]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)[0x7f7fd2185c37][ubuntu:05598]
[ 2]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x148)[0x7f622e18b028][ubuntu:05597]
[ 3]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x148)[0x7f7fd2189028][ubuntu:05598]
[ 3]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x155)[0x7fe484ccb535][ubuntu:05596]
[ 4]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x155)[0x7f622e9aa535][ubuntu:05597]
[ 4]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x155)[0x7f7fd29a8535][ubuntu:05598]
[ 4]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e6d6)[0x7fe484cc96d6][ubuntu:05596]
[ 5]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e6d6)[0x7f622e9a86d6][ubuntu:05597]
[ 5]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e6d6)[0x7f7fd29a66d6][ubuntu:05598]
[ 5]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e703)[0x7fe484cc9703][ubuntu:05596]
[ 6]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e703)[0x7f7fd29a6703][ubuntu:05598]
[ 6]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e703)[0x7f622e9a8703][ubuntu:05597]
[ 6]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e922)[0x7fe484cc9922][ubuntu:05596]
[ 7]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e922)[0x7f622e9a8922][ubuntu:05597]
[ 7]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e922)[0x7f7fd29a6922][ubuntu:05598]
[ 7]
/home/ernesto/programs/relion/build/lib/librelion_lib.so(_ZN7MpiNode16report_MPI_ERROREi+0x136)[0x7fe4854c6656][ubuntu:05596]
*** End of error message
***/home/ernesto/programs/relion/build/lib/librelion_lib.so(_ZN7MpiNode16report_MPI_ERROREi+0x136)[0x7f622f1a5656][ubuntu:05597]
*** End of error message
***/home/ernesto/programs/relion/build/lib/librelion_lib.so(_ZN7MpiNode16report_MPI_ERROREi+0x136)[0x7f7fd31a3656][ubuntu:05598]
*** End of error message ***terminate called after throwing an instance of
'RelionError'[ubuntu:05595] *** Process received signal ***[ubuntu:05595]
Signal: Aborted (6)[ubuntu:05595] Signal code:  (-6)[ubuntu:05595] [ 0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x10330)[0x7f94519ab330][ubuntu:05595]
[ 1]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)[0x7f945160cc37][ubuntu:05595]
[ 2]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x148)[0x7f9451610028][ubuntu:05595]
[ 3]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x155)[0x7f9451e2f535][ubuntu:05595]
[ 4]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e6d6)[0x7f9451e2d6d6][ubuntu:05595]
[ 5]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e703)[0x7f9451e2d703][ubuntu:05595]
[ 6]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5e922)[0x7f9451e2d922][ubuntu:05595]
[ 7]
/home/ernesto/programs/relion/build/lib/librelion_lib.so(_ZN7MpiNode16report_MPI_ERROREi+0x136)[0x7f945262a656][ubuntu:05595]
*** End of error message ****


Does anybody know what could be the issue?

Thank you in advance for the help,
Ernesto.