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relion5.0 update

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This commit is contained in:
assman_g
2024-04-03 16:13:27 +02:00
parent e44af53b40
commit d9d6ec9f98
4 changed files with 61 additions and 3 deletions
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2
EM/relion/README.md
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@@ -11,3 +11,5 @@ and MKL, but this would require additional openmpi variants.
After running ./build, install relion scripts from the repository at
https://git.psi.ch/lsm-hpce/relion-scripts
From version 5.0-beta on, a conda env is required. conda env is build in the folder $SRC\_DIR/conda\_envs. Also, weights for BLUSH, MODEL-ANGELO and CLASS-RANKER are downloaded in the installation step.

52
EM/relion/build
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@@ -2,11 +2,23 @@
pbuild::add_to_group 'EM'
pbuild::use_cmake
PROFILE="no"
SP="no"
pbuild::prep() {
local BRANCH
if [[ "$V" =~ beta$ ]]; then
BRANCH="ver${V_MAJOR}.${V_MINOR}"
elif [[ "$V" =~ profile$ ]]; then
BRANCH="${V_PKG}"
PROFILE="yes"
elif [[ "$V" =~ sp$ ]]; then
BRANCH="ver${V_MAJOR}.${V_MINOR}"
SP="yes"
else
BRANCH="${V_PKG}"
fi
@@ -15,6 +27,46 @@ pbuild::prep() {
}
pbuild::pre_configure() {
# Section will be switched on for -profile version
#-----------------------------------------------------------
if [[ "$PROFILE" == "yes" ]]; then
pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=BENCHMARKING"
fi
#------------------------------------------------------------
# Section will be switched on for single-precision version
# Safe memory usage for multibody refinements
#------------------------------------------------------------
if [[ "$SP" == "yes" ]]; then
pbuild::add_configure_args "-DDoublePrec_CPU=OFF"
fi
#------------------------------------------------------------
# The following section will only work for versions >= 5.0-beta
# -------------------------------------------------------------
if [[ "$V_MAJOR" -ge "5" ]]; then
#download blush weights
wget ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/blush_v1.0.ckpt.gz -P "$PREFIX/torch/hub/checkpoints/relion_blush" \
&& gunzip "$PREFIX/torch/hub/checkpoints/relion_blush/blush_v1.0.ckpt.gz"
mv "$PREFIX/torch/hub/checkpoints/relion_blush/blush_v1.0.ckpt" "$PREFIX/torch/hub/checkpoints/relion_blush/v1.0.ckpt"
touch "$PREFIX/torch/hub/checkpoints/relion_blush/v1.0_installed.txt"
#Set Torch Home
pbuild::add_configure_args "-DTORCH_HOME_PATH=$PREFIX/torch"
#Conda
conda env create -f "$SRC_DIR/environment.yml" -p "$PREFIX/conda_env/$P_$V"
pbuild::add_configure_args "-DPYTHON_EXE_PATH=$PREFIX/conda_env/$P_$V/bin/python"
fi
#---------------------------------------------------------------
# CMake-based build
pbuild::add_configure_args "-DFORCE_OWN_FFTW=ON"

4
EM/relion/files/variants
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@@ -13,4 +13,6 @@ relion/3.1.3 stable gcc/9.2.0 openmpi/4.0.5_slurm cuda/11.0.3 b:cmake/3.15.5 b:t
relion/4.0-beta deprecated gcc/9.2.0 openmpi/4.0.5_slurm cuda/11.0.3 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0
relion/4.0.0 unstable gcc/11.2.0 openmpi/4.1.3_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0
relion/4.0.1 unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0
relion/4.0.1-profile unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0
relion/5.0-beta unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 anaconda/2019.07
relion/5.0-sp unstable gcc/10.4.0 openmpi/4.1.4_slurm cuda/11.5.1 b:cmake/3.23.2 b:tiff/4.3.0 b:git/2.37.0 anaconda/2019.07

6
EM/relion/modulefile
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@@ -3,7 +3,7 @@
module-whatis "3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)"
module-url "https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page"
module-license "GPLv2 license"
module-maintainer "Spencer Bliven <spencer.bliven@psi.ch>"
module-maintainer "Greta Assmann <greta.assmann@psi.ch>"
module-help "
RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a
@@ -41,7 +41,9 @@ setenv RELION_SUMMOVIE_EXECUTABLE /opt/psi/EM/Summovie/1.0.2/bin/sum_movie_openm
setenv RELION_CTFFIND_EXECUTABLE /opt/psi/EM/ctffind4/4.1.8/bin/ctffind
setenv RELION_GCTF_EXECUTABLE /opt/psi/EM/Gctf/1.06/bin/Gctf
setenv RELION_RESMAP_EXECUTABLE /opt/psi/EM/ResMap/1.1.4/bin/ResMap
setenv RELION_TOPAZ_EXECUTABLE /opt/psi/EM/relion/5.0-sp/conda_env/5.0-beta/bin/topaz
setenv RELION_PYTHON_EXECUTABLE /opt/psi/EM/relion/5.0-sp/conda_env/5.0-beta/bin/python
setenv RELION_TORCH_HOME_PATH /opt/psi/EM/relion/5.0-sp/torch
# Version-specific variables
setenv RELION_QSUB_TEMPLATE /opt/psi/EM/relion/$V/scripts/multi_gpu.sh
setenv RELION_MOTIONCOR2_EXECUTABLE /opt/psi/EM/MotionCor2/1.4.0/bin/MotionCor2