# Objects

name: 1.33.40.submitTemplate
classname: String
creation: 2014-07-14 06:33:02
value:
#!/bin/bash
### Inherit all current environment variables
#PBS -V
### Job name
#PBS -N %(JOB_NAME)s
### Queue name
###PBS -q %(JOB_QUEUE)s
### Standard output and standard error messages
#PBS -k eo
### Specify the number of nodes and thread (ppn) for your job.
#PBS -l nodes=%(JOB_NODES)d:ppn=%(JOB_THREADS)d
### Tell PBS the anticipated run-time for your job, where walltime=HH:MM:SS
#PBS -l walltime=%(JOB_HOURS)d:00:00
# Use as working dir the path where qsub was launched
WORKDIR=$PBS_O_WORKDIR
#################################
### Set environment varible to know running mode is non interactive
export XMIPP_IN_QUEUE=1
### Switch to the working directory;
cd $WORKDIR
# Make a copy of PBS_NODEFILE 
cp $PBS_NODEFILE %(JOB_NODEFILE)s
# Calculate the number of processors allocated to this run.
NPROCS=`wc -l < $PBS_NODEFILE`
# Calculate the number of nodes allocated.
NNODES=`uniq $PBS_NODEFILE | wc -l`
### Display the job context
echo Running on host `hostName`
echo Time is `date`
echo Working directory is `pwd`
echo Using ${NPROCS} processors across ${NNODES} nodes
echo PBS_NODEFILE:
cat $PBS_NODEFILE
#################################

%(JOB_COMMAND)s


name: 140.211.hostPath
classname: String
creation: 2014-07-14 06:16:26
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 283.309.hostPath
classname: String
creation: 2014-07-14 06:36:12
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 392.418.hostPath
classname: String
creation: 2014-07-14 06:46:21
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 346.439.hostPath
classname: String
creation: 2014-07-14 06:53:30
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 392.466.hostPath
classname: String
creation: 2014-07-14 06:54:13
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 392.487.hostPath
classname: String
creation: 2014-07-14 07:06:36
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 514.methodsInfo
classname: String
creation: 2014-07-14 07:11:03
value:
Total particles extracted: 4565
                Enabled: 4565
                Disabled: 0
Maximun ZScore value: 5


name: 514.553.hostPath
classname: String
creation: 2014-07-14 07:11:03
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 653.685.hostPath
classname: String
creation: 2014-07-14 07:15:57
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 721.771.hostPath
classname: String
creation: 2014-07-14 07:41:28
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 721.792.hostPath
classname: String
creation: 2014-07-14 08:45:07
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 881.907.hostPath
classname: String
creation: 2014-07-14 11:25:55
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 1015.1039.hostPath
classname: String
creation: 2014-07-14 11:28:11
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 1143.1172.hostPath
classname: String
creation: 2014-07-14 11:36:00
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 1197._error
classname: String
creation: 2014-07-14 11:38:44
value:
Protocol failed: Process returned with code 1, command: mpirun -np 4 -bynode `which relion_refine_mpi` --ref Runs/001143_XmippProtFilterVolumes/output_volume.vol --healpix_order 2 --scale  --angpix 7.55200431543 --norm  --auto_refine  --offset_range 5.0 --o Runs/001197_ProtRelionRefine3D/extra/relion --oversampling 1 --auto_local_healpix_order 4 --split_random_halves  --sym c1 --i Runs/001197_ProtRelionRefine3D/input_particles.star --particle_diameter 2000.0 --flatten_solvent  --offset_step 2.0 --ini_high 60.0  --j 2


name: 1197.1245.hostPath
classname: String
creation: 2014-07-14 11:38:44
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 1197.1266.hostPath
classname: String
creation: 2014-07-14 11:43:41
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


name: 1197.1287.hostPath
classname: String
creation: 2014-07-14 11:50:23
value:
/home/josem/ScipionUserData/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial/Relion_Tutorial


