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Merge branch 'em' into 'master'

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New EM versions

See merge request Pmodules/buildblocks!150
This commit is contained in:
bliven_s
2020-11-18 21:12:50 +01:00
parent 7e5d91d9f4 3d0560a0f3
commit 7974687dae
16 changed files with 133 additions and 17 deletions
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6
EM/Gautomatch/Gautomatch Executable file
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@@ -0,0 +1,6 @@
#!/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 "$@"

10
EM/Gautomatch/README Normal file
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@@ -0,0 +1,10 @@
# 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/*

22
EM/Gautomatch/build Executable file
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#!/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() {
:
}

2
EM/Gautomatch/files/variants Normal file
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@@ -0,0 +1,2 @@
Gautomatch/0.53 stable
Gautomatch/0.56 stable

14
EM/Gautomatch/modulefile Normal file
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#%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 Unpublished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.
"

6
EM/Gctf/Gctf Executable file
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@@ -0,0 +1,6 @@
#!/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 "$@"

10
EM/Gctf/README Normal file
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@@ -0,0 +1,10 @@
# 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/*

22
EM/Gctf/build Executable file
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@@ -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() {
:
}

2
EM/Gctf/files/variants Normal file
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@@ -0,0 +1,2 @@
Gctf/0.50 stable
Gctf/1.06 stable

14
EM/Gctf/modulefile Normal file
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@@ -0,0 +1,14 @@
#%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.
"

18
EM/MotionCor2/README.md
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@@ -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 |

4
EM/MotionCor2/build
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@@ -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/
}

7
EM/MotionCor2/files/variants
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@@ -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

6
EM/relion/build
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@@ -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
}

2
EM/relion/files/variants
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@@ -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

5
EM/relion/modulefile
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@@ -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