From 67c09995ae1149892f10b357887ff25e9f151f3a Mon Sep 17 00:00:00 2001
From: Spencer Bliven <spencer.bliven@gmail.com>
Date: Mon, 30 Mar 2020 14:43:13 +0200
Subject: [PATCH] Document crYOLO/1.5.6_gpu build process

---
 EM/crYOLO/README.md                           | 14 ++++++++++
 EM/crYOLO/build                               | 27 ++-----------------
 EM/crYOLO/files/variants                      |  1 +
 EM/crYOLO/modulefile                          | 13 ++++-----
 .../2019.07/conda-env-defs/cryolo/README.md   | 10 +++++++
 .../2019.07/conda-env-defs/cryolo/cryolo.yml  | 14 ++++++++++
 6 files changed, 46 insertions(+), 33 deletions(-)
 create mode 100644 EM/crYOLO/README.md
 create mode 100644 Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md
 create mode 100644 Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo.yml

diff --git a/EM/crYOLO/README.md b/EM/crYOLO/README.md
new file mode 100644
index 0000000..9845306
--- /dev/null
+++ b/EM/crYOLO/README.md
@@ -0,0 +1,14 @@
+# crYOLO
+
+crYOLO/1.2.3 was built as a miniconda independent environment.
+Subsequent versions are deployed as central conda environments.
+This significantly changed the build process.
+
+## Adding New Versions
+
+To add a new version, first create the conda environment, as described in
+../../Programming/anaconda/2019.07/conda-env-defs/cryolo/.
+
+Next, update files/variants with the new version and run `./build <VERSION>` to
+install the modulefile
+
diff --git a/EM/crYOLO/build b/EM/crYOLO/build
index cc36cb6..6f1766a 100755
--- a/EM/crYOLO/build
+++ b/EM/crYOLO/build
@@ -3,14 +3,7 @@
 
 pbuild::add_to_group 'EM'
 pbuild::prep() {
-
-    source "${BUILDBLOCK_DIR}/files/config-$V.sh"
-
-    echo "prepping"
-    mkdir -p "$SRC_DIR"
-    curl -fsSLo "$SRC_DIR/miniconda.sh" "https://repo.anaconda.com/miniconda/${MINICONDA_VERSION:-Miniconda2-latest-Linux-x86_64.sh}"
-    curl -fsSLo "$SRC_DIR/cryoloBM.tgz" "${CRYOLOBM_URL:-ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_BM_V1_1_1/cryoloBM-1.1.1.tar.gz}"
-    curl -fsSLo "$SRC_DIR/cryolo.tgz" "${CRYOLO_URL:-ftp://ftp.gwdg.de/pub/misc/sphire/crYOLO_V${V_MAJOR}_${V_MINOR}_${V_PATCH}/cryolo-${V}.tar.gz}"
+    :
 }
 
 pbuild::configure() {
@@ -22,22 +15,6 @@ pbuild::compile() {
 }
 
 pbuild::install() {
-    mkdir -p $PREFIX
-
-    # Install conda
-    bash "$SRC_DIR/miniconda.sh" -b -p $PREFIX/conda
-
-    # Create environment
-    $PREFIX/conda/bin/conda create -y --name crYOLO anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy
-
-    # Activate
-    source $PREFIX/conda/bin/activate crYOLO
-
-    # Install
-    pip install $SRC_DIR/cryolo.tgz
-    pip install $SRC_DIR/cryoloBM.tgz
-
-    # Deactivate
-    source deactivate
+    :
 }
 
diff --git a/EM/crYOLO/files/variants b/EM/crYOLO/files/variants
index 942ddbb..7dc6e35 100644
--- a/EM/crYOLO/files/variants
+++ b/EM/crYOLO/files/variants
@@ -1,2 +1,3 @@
 crYOLO/1.2.3	unstable	cuda/9.0.176
+crYOLO/1.5.6_gpu	unstable	anaconda/2019.07
 
diff --git a/EM/crYOLO/modulefile b/EM/crYOLO/modulefile
index fbafb29..596f793 100644
--- a/EM/crYOLO/modulefile
+++ b/EM/crYOLO/modulefile
@@ -32,20 +32,17 @@ switch -- $shelltype {
     }
 }
 
-#puts stderr "Switching crYOLO mode to [module-info mode]"
-#puts stdout "{ date; echo Switching crYOLO mode to [module-info mode] ; } >> /gpfs/home/bliven_s/cryolo_mod.log;\n"
-
+#set useflag [string map {{:} {}} $USEFLAGS]
+#puts stderr "conda activate cryolo-${V_PKG}-${USEFLAGS%\n"
 
 switch [module-info mode] {
     "load" {
-        #puts stderr "source $PREFIX/conda/bin/activate crYOLO"
-        puts stdout "source $PREFIX/conda/bin/activate crYOLO;\n"
+      # Relies on the anaconda module being loaded since we need to update the path
+      puts stdout "conda activate cryolo-1.5.6-gpu;\n"
     }
     "unload" -
     "remove" {
-        #puts stderr "source deactivate"
-        puts stdout "source $PREFIX/conda/bin/deactivate;\n"
-        puts stdout {unset $(set|sed -rn 's/^(_?conda[a-z_]*).*$/\1/pI');}
+        puts stdout "conda deactivate;\n"
     }
 }
 
diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md b/Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md
new file mode 100644
index 0000000..46e620a
--- /dev/null
+++ b/Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md
@@ -0,0 +1,10 @@
+# INSTALLATION
+
+IMPORTANT! DON'T INSTALL WITH AURISTOR. Use an OpenAFS system (e.g. pmod6)
+
+    export TMPDIR=/opt/tmp/bliven_s
+    CONDA_COPY_ALWAYS=1 conda env create --file cryolo.yml
+    conda activate cryolo
+
+The alternate TMPDIR is required on pmod6 because /tmp is too small for pip to expand all wheel files.
+
diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo.yml b/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo.yml
new file mode 100644
index 0000000..42b1fe6
--- /dev/null
+++ b/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo.yml
@@ -0,0 +1,14 @@
+name: cryolo-1.5.6-gpu
+channels:
+  - defaults
+dependencies:
+  - python=3.6
+  - pyqt=5
+  - cudnn=7.1.2
+  - numpy==1.14.5
+  - cython
+  - wxPython==4.0.4
+  - intel-openmp==2019.4
+  - pip
+  - pip:
+    - cryolo[gpu]==1.5.6