Dear All,

I have been trying to proceed with Local symmetry in Relion.

In our environment I tried to run using R3.0 and R3.1

#!/bin/zsh
#SBATCH --partition all
#SBATCH --time 7-00:00
#SBATCH --constraint E5-2640&256G
#SBATCH --ntasks 80
#SBATCH --cpus-per-task 1
#SBATCH --error run.err
#SBATCH --output run.out
#SBATCH --job-name relion3i
#SBATCH --open-mode append
#SBATCH --no-requeue
#error SBATCH --export=NONE
#error SBATCH --export=LD_PRELOAD=""
export LD_PRELOAD=""

# run the job
echo "### start : $(date)  ###"
echo "### master: $(hostname)  ###"
echo "### jobid : ${SLURM_JOB_ID}  ###"
source /etc/profile.d/modules.sh
module use /beegfs/cssb/software/modulefiles/em
module load relion/3.0-icc2020-altcpu

# check myself if the relion gpu flag is off
FOUND=$(grep '\-\-gpu' ${0})
if [ $? -ne 1 ]; then
	echo "Warning: This is a CPU submission script template!"
	echo "Warning: It seems that the 'Use GPU acceleration' flag in the 
Relion 'Compute' tab is enabled."
	echo "ERROR: The Relion gpu flag is turned on - exiting!!!"
	exit 1
fi

mpirun --map-by node --mca opal_warn_on_missing_libcuda 0 \
	-n 80 relion_localsym_mpi--search --i_map run_ct13_class001.mrc 
--i_op_mask_info D1_2_masks.star --o_mask_info D1D2_iter000.star 
--angpix 0.87 --ang_step 5

echo "### end: $(date)  ###"


got this error


ERROR: ld.so: object 'libdlfaker.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libvglfaker.so' from LD_PRELOAD cannot be
preloaded: ignored.
CUDA 10.1 loaded
pocl warning: encountered incomplete implementation in
clGetDeviceInfo.c:169
[max-ferrari023:25272:0:25272] Caught signal 11 (Segmentation fault:
address not mapped to object at address (nil))

/beegfs/cssb/software/em/relion/3.0-icc2020-altcpu/src/matrix1d.h: [
Matrix1D<double>::resize() ]
        ...
        458         {
        459             T val;
        460             if (j >= vdim)
==>   461                 val = 0;
        462             else
        463                 val = vdata[j];
        464             new_vdata[j] = val;

==== backtrace (tid:  25272) ====
   0 0x0000000000478adb Matrix1D<double>::resize()
/beegfs/cssb/software/em/relion/3.0-icc2020-altcpu/src/matrix1d.h:461
   1 0x0000000000478adb Matrix1D<double>::initZeros()
/beegfs/cssb/software/em/relion/3.0-icc2020-altcpu/src/matrix1d.h:604
   2 0x0000000000478adb Localsym_composeOperator()
/beegfs/cssb/software/em/relion/3.0-icc2020-altcpu/src/local_symmetry.cpp:131
   3 0x0000000000429c39 local_symmetry_parameters_mpi::run()
/beegfs/cssb/software/em/relion/3.0-icc2020-altcpu/src/local_symmetry_mpi.cpp:93
   4 0x000000000041fe15 main()
/beegfs/cssb/software/em/relion/3.0-icc2020-altcpu/src/apps/localsym_mpi.cpp:10
   5 0x0000000000022505 __libc_start_main()  ???:0
   6 0x000000000041fc29 _start()  ???:0
=================================
[max-ferrari023:25272] *** Process received signal ***
[max-ferrari023:25272] Signal: Segmentation fault (11)
[max-ferrari023:25272] Signal code:  (-6)
[max-ferrari023:25272] Failing at address: 0x89c8000062b8
[max-ferrari023:25272] [ 0]
/lib64/libpthread.so.0(+0xf5f0)[0x2b42952455f0]
[max-ferrari023:25272] [ 1]
relion_localsym_mpi(_Z24Localsym_composeOperatorR8Matrix1DIdEddddddd+0x9b)[0x478adb]
[max-ferrari023:25272] [ 2]
relion_localsym_mpi(_ZN29local_symmetry_parameters_mpi3runEv+0x9e9)[0x429c39]
[max-ferrari023:25272] [ 3] relion_localsym_mpi(main+0x125)[0x41fe15]
[max-ferrari023:25272] [ 4]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b4295474505]
[max-ferrari023:25272] [ 5] relion_localsym_mpi[0x41fc29]
[max-ferrari023:25272] *** End of error message ***
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node max-ferrari023
exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------

when I tried the non-parallel mpi I got this one:
ERROR: ld.so: object 'libdlfaker.so' from LD_PRELOAD cannot be 
preloaded: ignored.
ERROR: ld.so: object 'libvglfaker.so' from LD_PRELOAD cannot be 
preloaded: ignored.
CUDA 10.1 loaded
pocl warning: encountered incomplete implementation in 
clGetDeviceInfo.c:169
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 7 with PID 38907 on node max-wn013 
exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
(base) 
[koubatom@max-cssb-display002]/beegfs/cssb/user/koubatom/LASV_C_R3p1/dimer%


Do you have any advice what could have gone wrong?

Thank you

Tomas

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