new file: p/PhaseLink/PhaseLink-20210503-fix-python-bin.patch

new file:   p/PhaseLink/PhaseLink-20210503-fosscuda-2020b.eb
	new file:   p/PhaseLink/PhaseLink-20210503.tar.gz
	deleted:    m/mpi4pyscf/mpi4pyscf-0.3.1.tar.gz
	deleted:    p/PySCF/PySCF-2.0.1-intel-2020b.eb.broken
	deleted:    q/QMCPACK/QMCPACK-3.12.0-intel-2020b-Python-3.8.6.eb.old
	deleted:    q/QMCPACK/QMCPACK-3.13.0-foss-2021a-Python-3.9.5.eb.broken
	deleted:    q/QMCPACK/QMCPACK-3.13.0-intel-2020b-Python-3.8.6.eb.old

p/PhaseLink/PhaseLink-20210503-fix-python-bin.patch

@@ -0,0 +1,48 @@
+diff -dur PhaseLink-20210503-orig/params.json PhaseLink-20210503/params.json
+--- PhaseLink-20210503-orig/params.json	2022-04-14 16:12:07.547992065 +0200
++++ PhaseLink-20210503/params.json	2022-04-14 16:17:21.079798445 +0200
+@@ -28,7 +28,7 @@
+     "lat_max": 37.0,
+     "lon_min": -121.0,
+     "lon_max": -115,
+-    "fault_file": "/home/zross/src/Qt_flt_v2-0latlonNAD27.MIF",
++    "fault_file": "src/Qt_flt_v2-0latlonNAD27.MIF",
+     "n_min_radius": 8,
+     "n_fake": 0,
+     "max_event_depth": 25.0,
+diff -dur PhaseLink-20210503-orig/phaselink_dataset.py PhaseLink-20210503/phaselink_dataset.py
+--- PhaseLink-20210503-orig/phaselink_dataset.py	2022-04-14 16:12:07.547992065 +0200
++++ PhaseLink-20210503/phaselink_dataset.py	2022-04-14 16:15:46.740759378 +0200
+@@ -1,4 +1,4 @@
+-#!/home/zross/bin/python
++#!/usr/bin/env python
+ import numpy as np
+ import multiprocessing as mp
+ import pickle
+diff -dur PhaseLink-20210503-orig/phaselink_eval.py PhaseLink-20210503/phaselink_eval.py
+--- PhaseLink-20210503-orig/phaselink_eval.py	2022-04-14 16:12:07.548992055 +0200
++++ PhaseLink-20210503/phaselink_eval.py	2022-04-14 16:15:59.125633226 +0200
+@@ -1,4 +1,4 @@
+-#! /home/zross/bin/python
++#!/usr/bin/env python
+ 
+ # PhaseLink: Earthquake phase association with deep learning
+ # Author: Zachary E. Ross
+diff -dur PhaseLink-20210503-orig/phaselink_plot.py PhaseLink-20210503/phaselink_plot.py
+--- PhaseLink-20210503-orig/phaselink_plot.py	2022-04-14 16:12:07.549992045 +0200
++++ PhaseLink-20210503/phaselink_plot.py	2022-04-14 16:16:12.931492600 +0200
+@@ -1,4 +1,4 @@
+-#!/home/zross/bin/python 
++#!/usr/bin/env python 
+ 
+ import numpy as np
+ import sys
+diff -dur PhaseLink-20210503-orig/phaselink_train.py PhaseLink-20210503/phaselink_train.py
+--- PhaseLink-20210503-orig/phaselink_train.py	2022-04-14 16:12:07.550992035 +0200
++++ PhaseLink-20210503/phaselink_train.py	2022-04-14 16:17:48.880515268 +0200
+@@ -1,4 +1,4 @@
+-#!/home/zross/bin/python
++#!/usr/bin/env python
+ import numpy as np
+ import os
+ import torch

p/PhaseLink/PhaseLink-20210503-fosscuda-2020b.eb

@@ -0,0 +1,46 @@
+# IT4Innovations
+# JK 2022
+
+easyblock = 'PackedBinary'
+
+name = 'PhaseLink'
+version = '20210503'
+
+local_pytorch_ver = '-PyTorch-1.10.0'
+
+homepage = 'https://github.com/interseismic/PhaseLink'
+description = """
+PhaseLink applies a deep learning approach to seismic phase association.
+"""
+
+toolchain = {'name': 'fosscuda', 'version': '2020b'}
+
+# clone from github and create an archive
+sources = ['%(name)s-%(version)s.tar.gz']
+extract_sources = True
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('apex', '20210420'),
+    ('CuPy', '8.5.0'),
+    ('Cython', '0.29.22'),
+    ('geopy', '2.1.0'),
+    ('h5py', '3.1.0'),
+    ('matplotlib', '3.3.3'),
+    ('mpi4py', '3.1.3', '', ('foss', '2020b')),
+    ('MPICH', '3.3.2'),
+    ('numba', '0.52.0'),
+    ('obspy', '1.3.0'),
+    ('pyproj', '3.0.1'),
+    ('PyTorch', '1.10.0'),
+    ('scikit-learn', '0.23.2'),
+    ('torchaudio', '0.10.0', local_pytorch_ver),
+    ('torchvision', '0.11.3', local_pytorch_ver),
+]
+
+postinstallcmds = ['find %(installdir)s -type f -name "*.py" -print0 | xargs -0 chmod +x']
+
+skipsteps = ['sanitycheck']
+modextrapaths = {'PYTHONPATH': ''}
+
+moduleclass = 'geo'

p/PySCF/PySCF-2.0.1-intel-2020b.eb.broken

@@ -1,49 +0,0 @@
-# has a problem with iimpi, doesn't work
-# IT4Innovations
-# JK 2022
-
-easyblock = 'CMakeMakeCp'
-
-name = 'PySCF'
-version = '2.0.1'
-
-homepage = 'http://www.pyscf.org'
-description = "PySCF is an open-source collection of electronic structure modules powered by Python."
-
-toolchain = {'name': 'intel', 'version': '2020b'}
-
-source_urls = ['https://github.com/pyscf/pyscf/archive/']
-sources = ['v%(version)s.tar.gz']
-checksums = ['6a152860787351aae52dc1ef2399bd9564fa314dca070312cfc0f2c3fc7412cf']
-
-builddependencies = [('CMake', '3.20.1')]
-
-dependencies = [
-    ('Python', '3.8.6'),
-    ('SciPy-bundle', '2020.11'),  # for numpy, scipy
-    ('h5py', '3.1.0'),
-    ('libcint', '4.4.0'),
-    ('libxc', '4.3.4'),
-    ('XCFun', '2.1.1'),
-]
-
-start_dir = 'pyscf/lib'
-
-separate_build_dir = True
-
-configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF"
-
-prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && "
-
-files_to_copy = ['pyscf']
-
-sanity_check_paths = {
-    'files': ['pyscf/__init__.py'],
-    'dirs': ['pyscf/data', 'pyscf/lib'],
-}
-
-sanity_check_commands = ["python -c 'import pyscf'"]
-
-modextrapaths = {'PYTHONPATH': ''}
-
-moduleclass = 'chem'

q/QMCPACK/QMCPACK-3.12.0-intel-2020b-Python-3.8.6.eb.old

@@ -1,64 +0,0 @@
-# IT4Innovations 2021
-# JK2021
-
-easyblock = 'CMakeMake'
-
-name = 'QMCPACK'
-version = '3.12.0'
-versionsuffix = "-Python-%(pyver)s"
-
-homepage = "https://qmcpack.org/"
-description = """QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code. Its main applications are electronic structure calculations of molecular, quasi-2D and solid-state systems. Variational Monte Carlo (VMC), diffusion Monte Carlo (DMC) and a number of other advanced QMC algorithms are implemented. Orbital space auxiliary field QMC (AFQMC) has recently been added. By directly solving the Schrodinger equation, QMC methods offer greater accuracy than methods such as density functional theory, but at a trade-off of much greater local_computational expense.
-"""
-
-# vypada to, ze od 3.12.0 uz optimalizace na avx2 nedela trable?
-toolchain = {'name': 'intel', 'version': '2020b'}
-import os
-if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
-   toolchainopts = {'opt': True, 'pic': True, 'usempi': True, 'optarch': 'march=core-avx2'}
-   prebuildopts = "echo %(builddir)s && while read i; do echo $i; sed 's|-xHost|-march=core-avx2|g' -i $i; done < <(grep xHost %(builddir)s -R | cut -d ':' -f 1 | sort -u) &&"
-else:
-   toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
-
-source_urls = ['https://github.com/QMCPACK/qmcpack/archive/']
-sources = ['v%(version)s.tar.gz']
-
-builddependencies = [('CMake', '3.20.1', '', True),]
-
-# odstran z module file GCC 9.3.0 - rovnak na intel
-dependencies = [
-    ('libxml2', '2.9.10'),
-    ('Boost', '1.74.0'),
-    ('HDF5', '1.10.7', '', ('iimpi', '2020b')),
-    ('Python', '3.8.6'),
-    ('h5py', '3.1.0'),
-    ('SciPy-bundle', '2020.11'),
-    ('GCC', '9.3.0', '', True),
-]
-
-separate_build_dir = True
-
-configopts = ' -DENABLE_SOA=1 '
-configopts += ' -DCMAKE_C_COMPILER=mpiicc -DCMAKE_CXX_COMPILER=mpiicpc '
-configopts += ' -DHDF5_PREFER_PARALLEL=1 -DENABLE_PHDF5=1 '
-configopts += ' -DQMC_SYMLINK_TEST_FILES=0 '
-configopts += ' -DCMAKE_BUILD_TYPE=Release '
-configopts += ' -DQMC_OMP=ON '
-
-# prekopiruje nexus knihovny o kterych install file tvrdi, ze nejsou potreba
-# ale evidentne to bez nich nejede
-preinstallopts = [
-		  ' mkdir -p %(installdir)s/nexus && ',
-		  ' cp -r %(builddir)s/qmcpack-%(version)s/nexus/lib %(installdir)s/nexus/lib && ',
-]
-
-
-# prida nexus knihovny do PYTHONPATH
-modextrapaths = {'PYTHONPATH': 'nexus/lib'}
-
-sanity_check_paths = {
-    'files': ['bin/qmcpack'],
-    'dirs': ['bin'],
-}
-
-moduleclass = 'phys'

q/QMCPACK/QMCPACK-3.13.0-foss-2021a-Python-3.9.5.eb.broken

@@ -1,71 +0,0 @@
-# This compilation is much slower than the intel one
-# IT4Innovations 2022
-# JK
-
-easyblock = 'CMakeMake'
-
-name = 'QMCPACK'
-version = '3.13.0'
-versionsuffix = "-Python-%(pyver)s-test"
-
-homepage = "https://qmcpack.org/"
-description = """QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code. Its main applications are electronic structure calculations of molecular, quasi-2D and solid-state systems. Variational Monte Carlo (VMC), diffusion Monte Carlo (DMC) and a number of other advanced QMC algorithms are implemented. Orbital space auxiliary field QMC (AFQMC) has recently been added. By directly solving the Schrodinger equation, QMC methods offer greater accuracy than methods such as density functional theory, but at a trade-off of much greater local_computational expense.
-"""
-
-toolchain = {'name': 'foss', 'version': '2021a'}
-import os
-if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
-   toolchainopts = {'opt': True, 'pic': True, 'usempi': True, 'optarch': 'march=core-avx2'}
-   prebuildopts = "echo %(builddir)s && while read i; do echo $i; sed 's|-xHost|-march=core-avx2|g' -i $i; done < <(grep xHost %(builddir)s -R | cut -d ':' -f 1 | sort -u) &&"
-else:
-   toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
-
-source_urls = ['https://github.com/QMCPACK/qmcpack/archive/']
-sources = ['v%(version)s.tar.gz']
-
-builddependencies = [('CMake', '3.20.1', '', True),]
-
-# odstran z module file GCC 9.3.0 - rovnak na intel
-dependencies = [
-    ('libxml2', '2.9.10'),
-    ('Boost', '1.76.0'),
-    ('HDF5', '1.10.7', '', ('gompi', '2021a')),
-    ('Python', '3.9.5'),
-    ('h5py', '3.2.1'),
-    ('SciPy-bundle', '2021.05'),
-    ('FFTW', '3.3.9', '', ('gompi','2021a')),
-    ('PySCF', '2.0.1'),
-#    ('GCC', '9.3.0', '', True),
-]
-
-separate_build_dir = True
-
-configopts = ' -DENABLE_SOA=1 '
-configopts += ' -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx '
-configopts += ' -DHDF5_PREFER_PARALLEL=1 -DENABLE_PHDF5=1 '
-configopts += ' -DQMC_SYMLINK_TEST_FILES=0 '
-configopts += ' -DCMAKE_BUILD_TYPE=Release '
-configopts += ' -DQMC_OMP=ON '
-configopts += ' -DCMAKE_INSTALL_PREFIX=%(installdir)s'
-configopts += ' -DINSTALL_NEXUS=ON '
-configopts += ' -DBUILD_UNIT_TESTS=ON -DBUILD_MICRO_BENCHMARKS=ON '
-configopts += ' -DBUILD_AFQMC=ON ' # FCIQMC fails
-
-# prekopiruje nexus knihovny o kterych install file tvrdi, ze nejsou potreba
-# ale evidentne to bez nich nejede
-
-preinstallopts = [
-    ' mkdir -p %(installdir)s/nexus && ',
-    ' mkdir -p %(installdir)s/QMCTools && ',
-    ' cp -r %(builddir)s/qmcpack-%(version)s/nexus %(installdir)s/ && ',
-    ' cp %(builddir)s/qmcpack-%(version)s/src/QMCTools/*.py %(installdir)s/QMCTools/ && ',
-]
-
-modextrapaths = {'PYTHONPATH': ['nexus/lib', 'QMCTools']}
-
-sanity_check_paths = {
-    'files': ['bin/qmcpack'],
-    'dirs': ['bin'],
-}
-
-moduleclass = 'phys'

q/QMCPACK/QMCPACK-3.13.0-intel-2020b-Python-3.8.6.eb.old

@@ -1,61 +0,0 @@
-# IT4Innovations 2022
-# JK
-
-easyblock = 'CMakeMake'
-
-name = 'QMCPACK'
-version = '3.13.0'
-versionsuffix = "-Python-%(pyver)s"
-
-homepage = "https://qmcpack.org/"
-description = """QMCPACK, is a modern high-performance open-source Quantum Monte Carlo (QMC) simulation code. Its main applications are electronic structure calculations of molecular, quasi-2D and solid-state systems. Variational Monte Carlo (VMC), diffusion Monte Carlo (DMC) and a number of other advanced QMC algorithms are implemented. Orbital space auxiliary field QMC (AFQMC) has recently been added. By directly solving the Schrodinger equation, QMC methods offer greater accuracy than methods such as density functional theory, but at a trade-off of much greater local_computational expense.
-"""
-
-toolchain = {'name': 'intel', 'version': '2020b'}
-import os
-if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
-   toolchainopts = {'opt': True, 'pic': True, 'usempi': True, 'optarch': 'march=core-avx2'}
-   prebuildopts = "echo %(builddir)s && while read i; do echo $i; sed 's|-xHost|-march=core-avx2|g' -i $i; done < <(grep xHost %(builddir)s -R | cut -d ':' -f 1 | sort -u) &&"
-else:
-   toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
-
-source_urls = ['https://github.com/QMCPACK/qmcpack/archive/']
-sources = ['v%(version)s.tar.gz']
-
-builddependencies = [('CMake', '3.20.1', '', True),]
-
-# odstran z module file GCC 9.3.0 - rovnak na intel
-dependencies = [
-    ('libxml2', '2.9.10'),
-    ('Boost', '1.74.0'),
-    ('HDF5', '1.10.7', '', ('iimpi', '2020b')),
-    ('Python', '3.8.6'),
-    ('h5py', '3.1.0'),
-    ('SciPy-bundle', '2020.11'),
-    ('GCC', '9.3.0', '', True),
-]
-
-separate_build_dir = True
-
-configopts = ' -DENABLE_SOA=1 '
-configopts += ' -DCMAKE_C_COMPILER=mpiicc -DCMAKE_CXX_COMPILER=mpiicpc '
-configopts += ' -DHDF5_PREFER_PARALLEL=1 -DENABLE_PHDF5=1 '
-configopts += ' -DQMC_SYMLINK_TEST_FILES=0 '
-configopts += ' -DCMAKE_BUILD_TYPE=Release '
-configopts += ' -DQMC_OMP=ON '
-
-# prekopiruje nexus knihovny o kterych install file tvrdi, ze nejsou potreba
-# ale evidentne to bez nich nejede
-preinstallopts = [
-		  ' mkdir -p %(installdir)s/nexus && ',
-		  ' cp -r %(builddir)s/qmcpack-%(version)s/nexus/lib %(installdir)s/nexus/lib && ',
-]
-
-modextrapaths = {'PYTHONPATH': 'nexus/lib'}
-
-sanity_check_paths = {
-    'files': ['bin/qmcpack'],
-    'dirs': ['bin'],
-}
-
-moduleclass = 'phys'