Hi Chris,

I believe it's a result of some missing macros/defineitions for some complex data types in different MPI flavors/versions. I had a case where someone solved this type of issue by changing line 77 of src/macros.h from

#define MY_MPI_COMPLEX MPI_DOUBLE_COMPLEX

to

#define MY_MPI_COMPLEX MPI_C_DOUBLE_COMPLEX

Let us know if that works for you too.

Cheers,

/Björn

​Ernesto,

Did you find a solution to your issues?

I'm getting the same error when compiling v2.0.5 (Ubuntu 16.04; CUDA 8.0 compiled at 52; openmpi 2.0.1; 4 x Titan X Pascal).  Compiling v2.0.3 stable on the same machine in the same way works without error.

Regards,

Chris

---

From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask]> on behalf of Ernesto Arias <[log in to unmask]>
Sent: 18 March 2017 00:24
To: [log in to unmask]
Subject: [ccpem] MPI error

 

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 datatype
terminate 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.

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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