Merge pull request #8 from sbamin/scratch

Scratch

Author: sbamin

confs/README.md

@@ -1,3 +1,3 @@
 ## Configuration files
 
-Configuration files used during setup. Read inline comments in respective configuration files for further details.
+Configuration files used during setup. These files are hard-coded with paths specific to my user env. Please edit those before applying to your user env. Also, read inline comments in respective configuration files for further details.

confs/hpc/mambaforge/envs/ben/etc/conda/activate.d/a01_warn_nongpu.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+# warn while activating Winter (GPU) env on Sumner (CPU) HPC.
+# load at the very beginning of activate.d/ scripts, e.g.,
+# a01_warn_nongpu.sh
+
+if [[ "$(hostname)" != *"winter"* ]]; then
+	echo -e "\n############### WARN: INVALID HPC ################
+\nhostname string, $(hostname) does not match winter.\nconda env, ${CONDA_DEFAULT_ENV} works only on the Winter GPU HPC." >& 2
+fi

confs/hpc/mambaforge/envs/ben/etc/conda/activate.d/a02_gpu_switch.sh

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+
+# name this script such that it loads after
+# conda activates cuda related configs, e.g.,
+# cupy_activate.sh
+
+## switch gpu env to meet conda specific env needs
+## only on Winter GPU HPC
+
+if [[ "$(hostname)" == *"winter"* ]]; then
+	# avoid exiting with non-zero exit status
+	# during bash startup but manually
+	# fix any errors, if any loading/unloading
+	# these modules
+
+	## deactivate default gpu env
+	module unload gpu/11.1.1 || true
+
+	## activate non-default gpu env for conda ben env
+	module load gpu/11.1.1_ben || true
+fi

confs/hpc/mambaforge/envs/ben/etc/conda/deactivate.d/z99_gpu_switch.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+## switch gpu env to meet conda specific env needs
+## load at the last in deactivate directory
+
+if [[ "$(hostname)" == *"winter"* ]]; then
+	module unload gpu/11.1.1_ben || true
+fi

confs/hpc/mambaforge/envs/rey/etc/conda/activate.d/a01_warn_nongpu.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+# warn while activating Winter (GPU) env on Sumner (CPU) HPC.
+# load at the very beginning of activate.d/ scripts, e.g.,
+# a01_warn_nongpu.sh
+
+if [[ "$(hostname)" != *"winter"* ]]; then
+	echo -e "\n############### WARN: INVALID HPC ################
+\nhostname string, $(hostname) does not match winter.\nconda env, ${CONDA_DEFAULT_ENV} works only on the Winter GPU HPC." >& 2
+fi

confs/hpc/mambaforge/envs/rey/etc/conda/activate.d/activate-r-env.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env sh
+
+# name this script such that it loads after
+# conda activates r-base using activate-r-base.sh
+
+## override ~/.Renviron which point to R from yoda env
+R_HOME="$CONDA_PREFIX/lib/R"
+R_ENVIRON_USER="/projects/verhaak-lab/amins/hpcenv/opt/R/confs/rey/Renviron"
+
+export R_HOME R_ENVIRON_USER

confs/hpc/mambaforge/envs/rey/etc/conda/activate.d/d01_gpu_switch.sh

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+
+# name this script such that it loads after
+# conda activates cuda related configs, e.g.,
+# cupy_activate.sh
+
+## switch gpu env to meet conda specific env needs
+## only on Winter GPU HPC
+
+if [[ "$(hostname)" == *"winter"* ]]; then
+	# avoid exiting with non-zero exit status
+	# during bash startup but manually
+	# fix any errors, if any loading/unloading
+	# these modules
+
+	## deactivate non-default gpu env, if any.
+	module unload gpu/11.1.1_ben || true
+
+	## activate default gpu env
+	module load gpu/11.1.1 || true
+fi

confs/hpc/mambaforge/envs/rey/etc/conda/deactivate.d/deactivate-r-env.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env sh
+
+## fall back to pre-existing R env
+unset R_HOME R_ENVIRON_USER

confs/hpc/mambaforge/envs/rey/etc/conda/deactivate.d/z99_gpu_switch.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+## switch gpu env to meet conda specific env needs
+## load at the last in deactivate directory
+
+if [[ "$(hostname)" == *"winter"* ]]; then
+	module unload gpu/11.1.1 || true
+fi

confs/hpc/mambaforge/envs/yoda/etc/conda/activate.d/a01_warn_noncpu.sh

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+
+# warn while activating Sumner (CPU) env on Winter (GPU) HPC.
+# load at the very beginning of activate.d/ scripts, e.g.,
+# a01_warn_noncpu.sh
+
+## PS: It's ok to use CPU env on GPU HPC as long as both HPCs
+## share identical base OS (CentOS7 in our case) and shared
+## system paths, e.g., /etc/, /usr/, /opt/, etc.
+
+if [[ "$(hostname)" != *"sumner"* ]]; then
+	echo -e "\n######### WARN: CAREFUL MANAGING CPU ENV #########
+\nhostname string, $(hostname) does not match sumner.\nconda env, ${CONDA_DEFAULT_ENV} should be managed using Sumner CPU HPC.\nAvoid installing or updating packages outside Sumner HPC env." >& 2
+fi