GROMACS container

containers/2_ApplicationSpecific/GROMACS/README.md

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+# Examples for using nvidia's GROMACS container
+
+GROMACS is an open-source software suite for high-performance molecular dynamics and output analysis.
+
+The interactive and Slurm examples use nvidia's container.
+The container supports nvidia GPUs, but is limited to a single node.
+
+The interactive examples follow the [Lysozyme in Water GROMACS tutorial](http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html)
+and the long Slurm example script does the same computations.
+
+The interacrive examples use "xmgrace" - instructions for buildind a grace
+container are below.
+This is NOT required to use nvidia's GROMACS container.  The sample Slurm
+scrtips do NOT need this.
+
+
+## Building a container with grace/xmgrace
+
+1. Start an interactive job in the debug queue
+see the [CCR documantation on Slurm jobs](https://docs.ccr.buffalo.edu/en/latest/hpc/jobs) for more information
+
+e.g.
+
+```bash
+salloc --cluster=ub-hpc --partition=debug --qos=debug --mem=0 --exclusive --time=01:00:00
+```
+
+2. Change to your build directory
+e.g.
+
+```bash
+cd /projects/academic/[YourGroupName]/GROMACS
+```
+
+Set the target directory for all your container images
+e.g.
+
+```bash
+CONTAINER_DIR="/projects/academic/[CCRgroupname]/Containers"
+```
+
+Make sure APPTAINER_TMPDIR and APPTAINER_CACHEDIR environment
+variables are set to sensible values
+
+```bash
+export APPTAINER_TMPDIR="${APPTAINER_TMPDIR:-${SLURMTMPDIR}/apptainer/tmp}"
+mkdir -p "${APPTAINER_TMPDIR}"
+export APPTAINER_CACHEDIR="${APPTAINER_CACHEDIR:-${SLURMTMPDIR}/apptainer}"
+mkdir -p "${APPTAINER_CACHEDIR}"
+```
+
+Download the .def file
+
+```bash
+#curl -L -o "grace.def" "https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/GROMACS/containers/2_ApplicationSpecific/GROMACS/grace.def"
+curl -L -o "grace.def" "https://raw.githubusercontent.com/ubccr/ccr-examples/refs/heads/main/containers/2_ApplicationSpecific/GROMACS/grace.def"
+```
+
+Build the grace container image
+
+```bash
+apptainer build "${CONTAINER_DIR}/grace-$(arch).sif" "grace.def"
+```
+
+Verify that the build was successful
+
+```bash
+apptainer run \
+ -B /projects:/projects,/scratch:/scratch,/util:/util,/vscratch:/vscratch \
+ --nv \
+ "${CONTAINER_DIR}/grace-$(arch).sif" \
+ grace -version
+```
+
+Sample output:
+
+> 
+> Grace-5.1.25
+> 
+> GUI toolkit: @(#)Motif Version 2.3.8
+> Xbae version: 46004
+> T1lib: 1.3.1p3-grace
+> FFT: FFTW
+> NetCDF support: on
+> libpng: 1.6.43
+> libjpeg: 80
+> Built: Mon Apr  8 10:40:41 2024 on Linux #191-Ubuntu SMP Fri Feb 2 13:55:07 UTC 2024 5.4.0-173-generic x86_64
+> Compiler flags: gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/grace-mFwzxU/grace-5.1.25=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/grace-mFwzxU/grace-5.1.25=/usr/src/grace-1:5.1.25-14 -I.. -I. -I../T1lib/t1lib  -Wdate-time -D_FORTIFY_SOURCE=3  -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lXmHTML -lXbae -lXm -lXpm -lXmu -lXt -lXext -lX11  -lSM -lICE  ../cephes/libcephes.a -lnetcdf -lfftw3 ../T1lib/libt1.a  -ljpeg -lpng -lz -ltirpc -lm  
+> 
+> Registered devices:
+> Dummy PostScript EPS MIF SVG PNM JPEG PNG Metafile 
+> 
+> (C) Copyright 1991-1995 Paul J Turner
+> (C) Copyright 1996-2015 Grace Development Team
+> All Rights Reserved
+
+
+## Example Scripts
+
+Provided in this repository are a couple of example GROMACS Slurm jobs.
+
+### Short Slurm example
+
+x86_64  
+[slurm_nvidia_GROMACS_short_example.bash](./slurm_nvidia_GROMACS_short_example.bash)
+
+ARM64  
+[slurm_ARM64_nvidia_GROMACS_short_example.bash](./slurm_ARM64_nvidia_GROMACS_short_example.bash)
+
+
+### Long Slurm example
+
+This example does all the computations from the [Lysozyme in Water GROMACS tutorial](http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html)
+
+x86_64  
+[slurm_nvidia_GROMACS_long_example.bash](./slurm_nvidia_GROMACS_long_example.bash)
+
+ARM64  
+[slurm_ARM64_nvidia_GROMACS_long_example.bash](./slurm_ARM64_nvidia_GROMACS_long_example.bash)
+

containers/2_ApplicationSpecific/GROMACS/grace.def

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+Bootstrap: docker
+From: ubuntu:24.04
+
+%post -c /bin/bash
+  # Set the timezone, if unset
+  test -h /etc/localtime || ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime
+
+  cp /etc/apt/sources.list /etc/apt/sources.list~
+  sed -E -i 's/^# deb-src /deb-src /' /etc/apt/sources.list
+  apt-get -y update
+
+  # Install man & man pages - this section can be removed if not needed
+  # NOTE: Do this before installing anything else so their man pages are installed
+  sed -e '\|/usr/share/man|s|^#*|#|g' -i /etc/dpkg/dpkg.cfg.d/excludes
+  DEBIAN_FRONTEND=noninteractive apt-get -y install apt-utils groff dialog man-db manpages manpages-posix manpages-dev
+  rm -f /usr/bin/man
+  dpkg-divert --quiet --remove --rename /usr/bin/man
+
+  # O/S package updates:
+  DEBIAN_FRONTEND=noninteractive apt-get -y upgrade
+
+  DEBIAN_FRONTEND=noninteractive apt-get -y install \
+   tzdata \
+   locales \
+   unzip \
+   wget \
+   git \
+   gawk \
+   pax-utils \
+   python3 \
+   python3-sphinx \
+   python3-sphinx-rtd-theme \
+   python-is-python3 \
+   grace \
+   curl \
+   less \
+   jq \
+   nano \
+   vim \
+   apt-file
+
+  # NOTE: apt-file is generally not needed to run, but can be useful during development
+  apt-file update
+
+  # These steps are necessary to configure Perl and can cause issues with Python if omitted
+  sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
+  dpkg-reconfigure --frontend=noninteractive locales
+  update-locale LANG=en_US.UTF-8
+
+%environment
+  export LANG=en_US.UTF-8
+  # Change the nvidia cache dir from ~/.nv/ComputeCache
+  export CUDA_CACHE_PATH="${SLURMTMPDIR:-/var/tmp}/nv_$(id -nu)"
+  mkdir -p "${CUDA_CACHE_PATH}"
+
+%runscript
+  #!/bin/bash
+  export PS1="xmgrace$ "
+  # Exec passed command (required for Modal ENTRYPOINT compatibility)
+  exec "$@"
+