Merge branch 'em' into 'master'

New EM versions

See merge request Pmodules/buildblocks!150

EM/Gautomatch/Gautomatch

+#!/bin/sh
+# Wrapper for Gautomatch on merlin
+module purge
+module use EM
+module load cuda/8.0.44 Gautomatch/0.56
+exec Gautomatch_v0.56_sm61_cu8.0 "$@"

EM/Gautomatch/README

+# Gautomatch
+
+## Installation
+
+1. Download binaries from https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/
+2. Update files/variants
+3. Run `./build <version>` to create directories
+4. Move all executables to /opt/psi/EM/Gautomatch/$VERSION/bin
+5. Create wrapper script at /opt/psi/EM/Gautomatch/$VERSION/bin/Gautomatch based on ./Gautomatch
+6. Fix permissions: chmod 755 /opt/psi/EM/Gautomatch/$VERSION/bin/*

EM/Gautomatch/build

+#!/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() {
+    :
+}
+

EM/Gautomatch/files/variants

+Gautomatch/0.53	stable
+Gautomatch/0.56	stable

EM/Gautomatch/modulefile

+#%Module1.0
+
+module-whatis           "Fully automatic accurate, convenient and extremely fast particle picking for EM"
+module-url              "https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/"
+module-license          "free"
+module-maintainer       "Spencer Bliven <spencer.bliven@psi.ch>"
+
+module-help     "
+Citation: Kai Zhang. Unpublished
+
+The `Gautomatch` script in this module includes the correct CUDA dependency. Other
+executables need CUDA loaded separately.
+"
+

EM/Gctf/Gctf

+#!/bin/sh
+# Wrapper for Gctf on merlin
+module purge
+module use EM
+module load cuda/8.0.44 Gctf/1.06
+exec Gctf-v1.06_sm_30_cu8.0_x86_64 "$@"

EM/Gctf/README

+# GCTF
+
+## Installation
+
+1. Download binaries from https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/
+2. Update files/variants
+3. Run `./build <version>` to create directories
+4. Move all executables to /opt/psi/EM/Gctf/$VERSION/bin
+5. Create wrapper script at /opt/psi/EM/Gctf/$VERSION/bin/Gctf based on ./Gctf
+6. Fix permissions: chmod 755 /opt/psi/EM/Gctf/$VERSION/bin/*

EM/Gctf/build

+#!/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() {
+    :
+}
+

EM/Gctf/files/variants

+Gctf/0.50	stable
+Gctf/1.06	stable

EM/Gctf/modulefile

+#%Module1.0
+
+module-whatis           "Real-time CTF determination and correction"
+module-url              "https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/zhang-software/"
+module-license          "free"
+module-maintainer       "Spencer Bliven <spencer.bliven@psi.ch>"
+
+module-help     "
+Citation: Zhang K. (2016). Gctf: Real-time CTF determination and correction. JSB, 193: 1-12.
+
+The `Gctf` script in this module includes the correct CUDA dependency. Other
+executables need CUDA loaded separately.
+"
+

EM/MotionCor2/README.md

@@ -10,12 +10,14 @@
 
 ## Cuda versions
 
-| MotionCor2 | Cuda Versions |
-|------------+---------------|
-| 1.0.5      | 8.0 9.1       |
-| 1.1.0      | 8.0 9.0 9.1   |
-| 1.2.0      | 8.0 9.1 9.2   |
-| 1.2.6      | 8.0 9.2 10.1  |
-| 1.3.0      | 8.0 9.2 10.1  |
-
+| MotionCor2 | Cuda Versions           |
+|------------+-------------------------|
+| 1.0.5      | 8.0 9.1                 |
+| 1.1.0      | 8.0 9.0 9.1             |
+| 1.2.0      | 8.0 9.1 9.2             |
+| 1.2.6      | 8.0 9.2 10.1            |
+| 1.3.0      | 8.0 9.2 10.1            |
+| 1.3.1      | 9.2 10.1 10.2           |
+| 1.3.2      | 8.0 9.2 10.0 10.1 10.2  |
+| 1.4.0      | 9.2 10.0 10.1 10.2 11.0 |
 

EM/MotionCor2/build

@@ -5,7 +5,7 @@
 pbuild::add_to_group 'EM'
 
 pbuild::prep() {
-    cp $BUILDBLOCK_DIR/files/LICENSE $PREFIX/
+    :
 }
 
 pbuild::configure() {
@@ -17,6 +17,6 @@ pbuild::compile() {
 }
 
 pbuild::install() {
-    :
+    cp $BUILDBLOCK_DIR/files/LICENSE $PREFIX/
 }
 

EM/MotionCor2/files/variants

@@ -3,5 +3,8 @@ MotionCor2/1.0.4	stable
 MotionCor2/1.0.5	stable	
 MotionCor2/1.1.0	stable	
 MotionCor2/1.2.0	stable	
-MotionCor2/1.2.6	unstable	
-MotionCor2/1.3.0	unstable	
+MotionCor2/1.2.6	stable	
+MotionCor2/1.3.0	stable	
+MotionCor2/1.3.1	stable	
+MotionCor2/1.3.2	stable	
+MotionCor2/1.4.0	stable	

EM/relion/build

@@ -22,7 +22,9 @@ pbuild::pre_configure() {
     pbuild::add_configure_args CudaTexture=ON
     pbuild::add_configure_args ALTCPU=ON
     pbuild::add_configure_args FORCE_OWN_TBB=ON
-    # Requires intel compiler
-    #pbuild::add_configure_args MKLFFT=ON
+    if [[ -n "$INTEL_VERSION" ]]; then
+        # Requires intel compiler
+        pbuild::add_configure_args MKLFFT=ON
+    fi
 }
 

EM/relion/files/variants

@@ -3,4 +3,6 @@ relion/3.0_beta	stable	gcc/4.9.4 openmpi/2.0.1 cuda/8.0.44
 relion/3.0.8	stable	gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/9.2.148 b:cmake/3.14.0 b:tiff/4.0.9
 relion/3.1-beta	unstable	gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/9.2.148 b:cmake/3.14.0 b:tiff/4.0.9
 relion/3.1.0	stable	gcc/7.5.0 openmpi/4.0.4_slurm cuda/10.0.130 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0
+relion/3.1.0-1	unstable	gcc/7.5.0 openmpi/4.0.4_slurm cuda/10.1.105 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0
+relion/3.1.1	unstable	gcc/9.3.0 openmpi/4.0.4_slurm cuda/11.0.3 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0
 

EM/relion/modulefile

@@ -43,6 +43,5 @@ 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
 
 # Version-specific variables
-setenv RELION_QSUB_TEMPLATE /opt/psi/EM/relion/3.1-beta/scripts/multi_gpu.sh
-setenv RELION_MOTIONCOR2_EXECUTABLE /opt/psi/EM/MotionCor2/1.3.0/bin/MotionCor2_1.3.0-Cuda92
-
+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_1.4.0_Cuda110