RunningXmippOnBlueGeneMartinsried

Running xmipp on BlueGene/P in Martinsried (genius1)

Running xmipp protocols

The xmipp protocols work onBlueGene, although the gui for these protocols (via xmipp_protocols) does not. That is because python-tk (Tkinter) is not installed. To run a protocol, make a job script like this:

#!/bin/bash
#
# @ job_name = xmipp_protocol_ml3d
# @ error = $(job_name).$(jobid).err
# @ output = $(job_name).$(jobid).out
# @ environment = COPY_ALL
# @ wall_clock_limit = 24:00:00
# @ notification = always
# @ notify_user = haller@biochem.mpg.de
# @ job_type = bluegene
# @ bg_size = 128
# @ bg_connection = PREFER_TORUS
# @ queue
#

# go to your project directory
cd ~/26S_xmipp/

export PATH=/u/thaller/BlueGene/xmipp/bin:$PATH
python xmipp_protocol_ml2d.py

And in the protocol, use

MyNumberOfCPUs=-1
MyMachineFile="USE_BG_SMP"

Note that in order to have this work, theapplications/scripts/protocols/launch_parallel_job.py file needs to be modified. See theBlueGeneAdaptedLaunchParralelJob file.

Running xmipp command-line programs

To run an xmipp command-line program that has been implemented with threads (ml2d, ml3d etc), prepare your job script as follows:

#!/bin/bash
#
# @ job_name = xmipp_protocol_ml3d
# @ error = $(job_name).$(jobid).err
# @ output = $(job_name).$(jobid).out
# @ environment = COPY_ALL
# @ wall_clock_limit = 24:00:00
# @ notification = always
# @ notify_user = haller@biochem.mpg.de
# @ job_type = bluegene
# @ bg_size = 128
# @ bg_connection = PREFER_TORUS
# @ queue
#

# go to your directory
cd ~/small_tagcase/
mkdir -p out
mpirun -mode SMP ~/xmipp/bin/xmipp_mpi_ml_align2d -i all_images.sel -ref seeds.sel -o out/std -iter 10 -thr 3

Or if the program does not have threads, you may use a script like the following:

#!/bin/bash
#
# @ job_name = xmipp_protocol_ml3d
# @ error = $(job_name).$(jobid).err
# @ output = $(job_name).$(jobid).out
# @ environment = COPY_ALL
# @ wall_clock_limit = 24:00:00
# @ notification = always
# @ notify_user = haller@biochem.mpg.de
# @ job_type = bluegene
# @ bg_size = 128
# @ bg_connection = PREFER_TORUS
# @ queue
#

# go to your directory
cd ~/small_tagcase/
mkdir -p out
mpirun -mode VN ~/xmipp/bin/xmipp_mpi_mlf_align2d -i all_images.sel -ref seeds.sel -o out/std -iter 10 -ctfdat all_images.ctfdat -high 20 -ini_high 60

--Main.SjorsScheres - 12 Feb 2009