ResMap (Resolution Map) is a Python (NumPy/SciPy) application with a Tkinter GUI and a command-line interface. It is a software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo- EM).

References:

• A. Kucukelbir, F.J. Sigworth, H.D. Tagare. Quantifying the Local Resolution of Cryo-EM Density Maps. Nature Methods, Volume 11, Issue 1, Pages 63-65, 2014.

• ResMap Main Site: http://resmap.sourceforge.net/
• ResMap PDF: ResMap-manual_v-1.95.pdf

• Module Name: ResMap (see the modules page for more information)

This application requires an X-Windows connection. Users are encouraged to use NX as their X11 servers.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --gres=gpu:p100:1
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load ResMap

[user@cn3144 ~]$ ResMap

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

After typing 'ResMap' at the prompt, input is menu-driven.

The correct path for the CUDA library file is /opt/resmap/ResMap_krnl-cuda-V9.0.102-sm35_gpu.so. You will need to update the GUI.

Create a batch input file (e.g. ResMap.sh). ResMap can be run without the need for an X11 server by starting a dummy X11 server with Xvfb and setting the $DISPLAY variable to a bogus number.

#!/bin/bash
module load ResMap
Xvfb -shmem -screen 0 1280x1024x24 &
export DISPLAY=":0"
cp $RESMAP_EXAMPLES/*.map .
ResMap --doBenchMarking --noguiSplit \
  emd_8731_half_map_1.map emd_8731_half_map_2.map

Submit this job using the Slurm sbatch command.

sbatch --mem=10 ResMap.sh

ResMap can be accelerated at least 10-fold by using GPUs rather than CPUs. This requires three options, --use_gpu, --set_gpu and --lib_krnl_gpu. Here is a batch script for doing so:

#!/bin/bash
module load ResMap
Xvfb -shmem -screen 0 1280x1024x24 &
export DISPLAY=":0"
cp $RESMAP_EXAMPLES/*.map .
ResMap --doBenchMarking --noguiSplit \
  emd_8731_half_map_1.map emd_8731_half_map_2.map \
  --use_gpu=yes --set_gpu=0 \
  --lib_krnl_gpu=/opt/resmap/ResMap_krnl-cuda-V9.0.102-sm35_gpu.so

Submit this job using this Slurm command, allocating a single GPU for the job:

sbatch --mem=10 --gres=gpu:p100:1 ResMap.sh