Submitting to SGE

Hello,

I am having trouble executing multiple jobs in parallele on our SGE cluster.
I am using the below specified mparameters and running frealign_run_refine on the head node. As expected 30 Jobs are queued and start runnning. One exemplary log file (the other 29 are the same):

scratch/test_c5_mult_refine_n_r1.log_1_708:

/bcm/opt/cryo/frealign/frealign_v9.11/bin/frealign_v9.exe: Command not found.


The path is correct, I already checked this.

mparameters:

# Computer-specific setting
cluster_type sge ! Set to "sge", "lsf", "slurm" or "pbs" when running on an SGE, LSF, SLURM or PBS cluster, otherwise set to "none".
nprocessor_ref 30 ! Number of CPUs to use during refinement.
nprocessor_rec 4 ! Number of CPUs to use during reconstruction.
mem_per_cpu 2000 ! Memory available per CPU (in MB).

# Refinement-specific parameters
MODE 1 ! 1, 2, 3 or 4. Refinement mode, normally 1. Set to 2 for additional search.
start_process 63 ! First cycle to execute. Output files from previous cycle (n-1) required.
end_process 63 ! Last cycle to execute.
res_high_refinement 15.0 ! High-resolution limit for particle alignment.
res_high_class 21.0 ! High-resolution limit to calculate class membership (OCC).
thresh_reconst 0.9 ! Particles with scores below this value will not be included in the reconstruction.
nclasses 1 ! Number of classes to use.

# Search-specific parameters
res_search 19.0 ! High-resolution limit for orientational search.
thresh_refine 70.0 ! Score threshold above which search will not be performed.
DANG 5.0 ! Angular step for orientational search.
ITMAX 200 ! Number of repetitions of grid search with random starting angles.
Bsearch 2000.0 ! B-factor filtering (when > 0) applied during search.

# Dataset-specific parameters
data_input test_c5 ! Root name for parameter and map files.
raw_images test_stack_c5_dc3
image_contrast N ! N or P. Set to N if particles are dark on bright background, otherwise set to P.
outer_radius 200.0 ! Outer radius of spehrical particle mask in Angstrom.
inner_radius 0.0 ! Inner radius of spehrical particle mask in Angstrom.
mol_mass 1500.0 ! Molecular mass in kDa of particle or helical segment.
Symmetry C1 ! Symmetry of particle.
pix_size 3.252 ! Pixel size of particle in Angstrom.
dstep 42.0 ! Pixel size of detector in micrometer.
Aberration 2.7 ! Sherical aberration coefficient in millimeter.
Voltage 300.0 ! Beam accelleration voltage in kilovolt.
Amp_contrast 0.1 ! Amplitude contrast.

# Expert parameters (for expert users)
XSTD 0.0 ! Tighter masking of 3D map (XSTD > 0) or particles (XSTD < 0).
PBC 20.0 ! Discriminate particles with different scores during reconstruction. Small values (5 - 10) discriminate more than large values (50 - 100).
refineangleinc 1 ! When larger than 1: Alternate between refinement of OCC and OCC + angles.
refineshiftinc 1 ! When larger than 1: Alternate between refinement of OCC and OCC + angles + shifts.
res_reconstruction 0.0 ! High-resolution limit of reconstruction. Normally set to Nyquist limit.
res_low_refinement 0.0 ! Low-resolution limit for particle alignment. Set to particle dimention or larger.
FMAG F ! T or F. Set to T to refine particle magnification. Not recommended in most cases.
FDEF F ! T or F. Set to T to refine defocus per micrograph. Not recommended in most cases.
FASTIG F ! T or F. Set to T to refine astigmatism. Not recommended in most cases.
FPART F ! T or F. Set to T to refine defocus for each particle. Not recommended in most cases.
FFILT T ! T or F. Set to T to apply optimal filter to reconstruction. Recommended in most cases.
FMATCH F ! T or F. Set to T to output matching projections. Only needed for diagnostics.
FBEAUT F ! T or F. Set to T to apply symmetry also in real space. Not needed in most cases.
FBOOST F ! T or F. Set to T to allow potential overfitting during refinement. Not recommended in most cases.
RBfactor 0.0 ! B-factor sharpening (when < 0) applied during refinement. Not recommended in most cases.
mp_cpus 1 ! Number of CPUs to use for each reconstruction job.
restart_after_crash F ! T or F. Set to T to restart job if it crashes.
delete_scratch T ! Delete intermediate files in scratch directory.
qsub_string_ref "-pe all.pe 1 -cwd -S /bin/bash" ! String to add to cluster jobs submitted for refinement (only for SGE and PBS clusters).
qsub_string_rec "-pe all.pe 1 -cwd -S /bin/bash" ! String to add to cluster jobs submitted for reconstruction (only for SGE and PBS clusters).
first_particle
last_particle
frealign_bin_dir /bcm/opt/cryo/frealign/frealign_v9.11/bin
scratch_dir