From 451d3db6f4c1f6d3542164071082e89daf97ef5d Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Thu, 10 Dec 2020 15:00:41 +0100 Subject: [PATCH 1/2] Add cisTEM modulefile No new versions are available --- EM/cisTEM/README | 16 +++++++++ EM/cisTEM/build | 22 +++++++++++++ .../files/settings/2018-06-30_settings.sh | 17 ++++++++++ .../files/settings/2019-11-04_settings.txt | 33 +++++++++++++++++++ EM/cisTEM/files/settings/settings.txt | 1 + EM/cisTEM/files/variants | 1 + EM/cisTEM/modulefile | 12 +++++++ 7 files changed, 102 insertions(+) create mode 100644 EM/cisTEM/README create mode 100755 EM/cisTEM/build create mode 100644 EM/cisTEM/files/settings/2018-06-30_settings.sh create mode 100644 EM/cisTEM/files/settings/2019-11-04_settings.txt create mode 120000 EM/cisTEM/files/settings/settings.txt create mode 100644 EM/cisTEM/files/variants create mode 100644 EM/cisTEM/modulefile diff --git a/EM/cisTEM/README b/EM/cisTEM/README new file mode 100644 index 0000000..ad9a4dd --- /dev/null +++ b/EM/cisTEM/README @@ -0,0 +1,16 @@ +# CisTEM + +## Installation + +1. Download binaries from https://cistem.org/ +2. Update files/variants +3. Run `./build ` to create directories +4. Move all executables to /opt/psi/EM/cisTEM/$VERSION/bin +5. Copy/link files: + + cisTEM_preallocate + cisTEM_preallocate132 -> cisTEM_preallocate + cisTEM_preallocate44 -> cisTEM_preallocate + default_run_profiles.txt -> ../settings/settings.txt + +6. Fix permissions: chmod 755 /opt/psi/EM/cisTEM/$VERSION/bin/* diff --git a/EM/cisTEM/build b/EM/cisTEM/build new file mode 100755 index 0000000..e57a477 --- /dev/null +++ b/EM/cisTEM/build @@ -0,0 +1,22 @@ +#!/usr/bin/env modbuild + +# Binary distribution with manual installation. See README.md + +pbuild::add_to_group 'EM' + +pbuild::prep() { + : +} + +pbuild::configure() { + : +} + +pbuild::compile() { + : +} + +pbuild::install() { + : +} + diff --git a/EM/cisTEM/files/settings/2018-06-30_settings.sh b/EM/cisTEM/files/settings/2018-06-30_settings.sh new file mode 100644 index 0000000..f5f16bf --- /dev/null +++ b/EM/cisTEM/files/settings/2018-06-30_settings.sh @@ -0,0 +1,17 @@ +number_of_profiles=2 +profile_0_name="slurm_128" +profile_0_manager_command="nohup /afs/psi.ch/sys/psi.merlin/EM/cisTEM/1.0.0/cistem-1.0.0-beta/$command" +profile_0_gui_address="" +profile_0_controller_address="" +profile_0_number_of_run_commands=1 +profile_0_command_0_command_to_run="sbatch /afs/psi.ch/sys/psi.merlin/EM/cisTEM/1.0.0/cistem-1.0.0-beta/slurm.sh $command" +profile_0_command_0_number_of_copies=128 +profile_0_command_0_delay_time_in_ms=10 +profile_1_name="slurm_32" +profile_1_manager_command="nohup /afs/psi.ch/sys/psi.merlin/EM/cisTEM/1.0.0/cistem-1.0.0-beta/$command" +profile_1_gui_address="" +profile_1_controller_address="" +profile_1_number_of_run_commands=1 +profile_1_command_0_command_to_run="sbatch /afs/psi.ch/sys/psi.merlin/EM/cisTEM/1.0.0/cistem-1.0.0-beta/slurm.sh $command" +profile_1_command_0_number_of_copies=32 +profile_1_command_0_delay_time_in_ms=10 diff --git a/EM/cisTEM/files/settings/2019-11-04_settings.txt b/EM/cisTEM/files/settings/2019-11-04_settings.txt new file mode 100644 index 0000000..d7d499f --- /dev/null +++ b/EM/cisTEM/files/settings/2019-11-04_settings.txt @@ -0,0 +1,33 @@ +number_of_profiles=4 +profile_0_name="preallocated 44cpu" +profile_0_manager_command="/opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/preallocated.sh $command" +profile_0_gui_address="" +profile_0_controller_address="" +profile_0_number_of_run_commands=1 +profile_0_command_0_command_to_run="/opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/preallocated.sh $command" +profile_0_command_0_number_of_copies=43 +profile_0_command_0_delay_time_in_ms=10 +profile_1_name="preallocated 132cpu" +profile_1_manager_command="/opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/preallocated.sh $command" +profile_1_gui_address="" +profile_1_controller_address="" +profile_1_number_of_run_commands=1 +profile_1_command_0_command_to_run="/opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/preallocated.sh $command" +profile_1_command_0_number_of_copies=131 +profile_1_command_0_delay_time_in_ms=10 +profile_2_name="allocate 44cpu" +profile_2_manager_command="sbatch --ntasks=44 --job-name=cisTEM --partition=daily --cpus-per-task=2 /opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/slurm.sh $command" +profile_2_gui_address="" +profile_2_controller_address="" +profile_2_number_of_run_commands=1 +profile_2_command_0_command_to_run="srun -n 1 -c 2 $command" +profile_2_command_0_number_of_copies=43 +profile_2_command_0_delay_time_in_ms=10 +profile_3_name="allocate 132cpu" +profile_3_manager_command="sbatch --ntasks=132 --job-name=cisTEM --partition=daily --cpus-per-task=2 /opt/psi/EM/cisTEM/1.0.0/cistem-1.0.0-beta/slurm.sh $command" +profile_3_gui_address="" +profile_3_controller_address="" +profile_3_number_of_run_commands=1 +profile_3_command_0_command_to_run="srun -n 1 -c 2 $command" +profile_3_command_0_number_of_copies=131 +profile_3_command_0_delay_time_in_ms=10 diff --git a/EM/cisTEM/files/settings/settings.txt b/EM/cisTEM/files/settings/settings.txt new file mode 120000 index 0000000..d2c886b --- /dev/null +++ b/EM/cisTEM/files/settings/settings.txt @@ -0,0 +1 @@ +2019-11-04_settings.txt \ No newline at end of file diff --git a/EM/cisTEM/files/variants b/EM/cisTEM/files/variants new file mode 100644 index 0000000..622b224 --- /dev/null +++ b/EM/cisTEM/files/variants @@ -0,0 +1 @@ +cistem/1.0.0 stable diff --git a/EM/cisTEM/modulefile b/EM/cisTEM/modulefile new file mode 100644 index 0000000..bafad09 --- /dev/null +++ b/EM/cisTEM/modulefile @@ -0,0 +1,12 @@ +#%Module1.0 + +module-whatis "cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them." +module-url "https://cistem.org" +module-license "3-clause BSD " +module-maintainer "Spencer Bliven " + +module-help " +cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. It was developed by Tim Grant, Alexis Rohou and Nikolaus Grigorieff and comprises a number of tools to process image data including movies, micrographs and stacks of single-particle images, implementing a complete “pipeline” of processing steps to obtain high-resolution single-particle reconstructions. +" + +prepend-path PATH $PREFIX/cistem-1.0.0-beta From 51436c81663c152a37c1a637771f4f066481fa94 Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Fri, 11 Dec 2020 15:28:02 +0100 Subject: [PATCH 2/2] Adding preallocated scripts --- EM/cisTEM/cisTEM_preallocate | 22 ++++++++++++++++++++++ EM/cisTEM/preallocated.sh | 9 +++++++++ 2 files changed, 31 insertions(+) create mode 100755 EM/cisTEM/cisTEM_preallocate create mode 100755 EM/cisTEM/preallocated.sh diff --git a/EM/cisTEM/cisTEM_preallocate b/EM/cisTEM/cisTEM_preallocate new file mode 100755 index 0000000..6803350 --- /dev/null +++ b/EM/cisTEM/cisTEM_preallocate @@ -0,0 +1,22 @@ +#!/bin/bash +# Launch script for running cisTEM with the 'preallocated_44cpu' profile + +# Default arguments +args=() +if [[ ! "${@}" =~ -t|--time ]]; then + args+=(--time=08:00:00) +fi +if [[ ! "${@}" =~ -p|--partition ]]; then + args+=(--partition=daily) +fi +if [[ ! "${@}" =~ -n|--ntasks ]]; then + # Take number of tasks from the script name + DEFAULT_TASKS="$(echo "$0"|sed -rn 's/.*[^0-9]([0-9]+$)/\1/p')" + args+=(--ntasks="${DEFAULT_TASKS:-44}") +fi +if [[ ! "${@}" =~ -c|--cpus-per-task ]]; then + args+=(--cpus-per-task=2) +fi + +exec interactive "${args[@]}" "$@" + diff --git a/EM/cisTEM/preallocated.sh b/EM/cisTEM/preallocated.sh new file mode 100755 index 0000000..7fb4023 --- /dev/null +++ b/EM/cisTEM/preallocated.sh @@ -0,0 +1,9 @@ +#!/bin/bash +# Wrapper for the 'preallocated' default profiles +# usage in cistem profile: preallocated.sh $command +set -e + +# Ensure we actually allocated resources +: "${SLURM_NODELIST:?Error: No nodes preallocated! See https://intranet.psi.ch/BIO/ComputingCisTEM}" + +srun -N 1 -n 1 -c 2 --exclusive $@