From 8b5b606f19286672fc9620406bc4b7d6fba08c26 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Wed, 11 Dec 2024 12:06:01 +0100
Subject: [PATCH 01/20] start host mpi injection

---
 .../install_openmpi_host_injection.sh         | 209 ++++++++++++++++++
 1 file changed, 209 insertions(+)
 create mode 100644 scripts/mpi_support/install_openmpi_host_injection.sh

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
new file mode 100644
index 0000000000..79cc428099
--- /dev/null
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -0,0 +1,209 @@
+#!/usr/bin/env bash
+
+# This script can be used to install the host MPI libraries under the `.../host_injections` directory.
+# It allows EESSI software to use the MPI stack from the host.
+#
+# The `host_injections` directory is a variant symlink that by default points to
+# `/opt/eessi`, unless otherwise defined in the local CVMFS configuration (see
+# https://cvmfs.readthedocs.io/en/stable/cpt-repo.html#variant-symlinks). For the
+# installation to be successful, this directory needs to be writeable by the user
+# executing this script.
+
+# Initialise our bash functions
+TOPDIR=$(dirname $(realpath $BASH_SOURCE))
+source "$TOPDIR"/../../utils.sh
+
+
+# Function to display help message
+show_help() {
+    echo "Usage: $0 [OPTIONS]"
+    echo "Options:"
+    echo "  --help                           Display this help message"
+    echo "  --mpi-path /path/to/mpi          Specify the path to the MPI host installation"
+	echo "  --pmix-path /path/to/mpi         Specify the path to the PMIX host installation"
+    echo "  -t, --temp-dir /path/to/tmpdir   Specify a location to use for temporary"
+    echo "                                   storage during the mpi injection"
+    echo "                                   (must have >10GB available)"
+}
+
+
+# Global associative array with os-release info
+declare -A OS_RELEASE
+
+get_os_release() {
+    local key
+    local value
+
+    while read -r key value; do
+	OS_RELEASE[${key}]="${value}"
+    done < <(awk -F = 'gsub(/"/, "", $2); {print $1, $2}' /etc/os-release)
+}
+
+
+parse_cmdline() {
+	while [[ $# -gt 0 ]]; do
+		case "$1" in
+			--help)
+				show_help
+				exit 0
+				;;
+			--mpi-path)
+				if [ -n "$2" ]; then
+					MPI_PATH="$2"
+					shift 2
+				else
+					echo "Error: Argument required for $1"
+					show_help
+					exit 1
+				fi
+				;;
+			--pmix-path)
+				if [ -n "$2" ]; then
+					PMIX_PATH="$2"
+					shift 2
+				else
+					echo "Error: Argument required for $1"
+					show_help
+					exit 1
+				fi
+				;;
+			-t|--temp-dir)
+				if [ -n "$2" ]; then
+					TEMP_DIR="$2"
+					shift 2
+				else
+					echo "Error: Argument required for $1"
+					show_help
+					exit 1
+				fi
+				;;
+			*)
+				show_help
+				fatal_error "Error: Unknown option: $1"
+				;;
+		esac
+	done
+}
+
+
+# ****Warning: patchelf v0.18.0 (currently shipped with EESSI) does not work.****
+# We get v0.17.2
+download_patchelf() {
+    local patchelf_version="0.17.2"
+    local url
+
+    url="https://github.com/NixOS/patchelf/releases/download/${patchelf_version}/"
+    url+="patchelf-${patchelf_version}-${EESSI_CPU_FAMILY}.tar.gz"
+
+    curl ${url} ${CURL_OPTS} -o ${TEMP_DIR}/patchelf.tar.gz
+    tar -xf ${TEMP_DIR}/patchelf.tar.gz -C ${TEMP_DIR}
+    PATCHELF_BIN=${TEMP_DIR}/bin/patchelf
+}
+
+
+inject_mpi() {
+    local efa_path="${AMAZON_PATH}/efa"
+    local openmpi_path="${MPI_PATH}"
+    local pmix_path="${PMIX_PATH}"
+
+    local eessi_ldd="${EESSI_EPREFIX}/usr/bin/ldd"
+    local system_ldd="/usr/bin/ldd"
+
+    (( OPENMPI_VERSION == 5 )) && openmpi_path+=5
+
+    local host_injection_mpi_path
+
+	host_injection_mpi_path=${EESSI_SOFTWARE_PATH/versions/host_injections}
+    host_injection_mpi_path+="/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}"
+    host_injection_mpi_path+="/rpath_overrides/OpenMPI/system/lib"
+
+    if [ -d ${host_injection_mpi_path} ]; then
+		echo "MPI was already injected"
+		return 0
+    fi
+
+    sudo mkdir -p ${host_injection_mpi_path}
+
+    local temp_inject_path="${TEMP_DIR}/mpi_inject"
+    mkdir ${temp_inject_path}
+
+    # Get all library files from efa and openmpi dirs
+    find ${efa_path} ${openmpi_path} ${pmix_path} -maxdepth 2 -type f -name "*.so*" -exec cp {} ${temp_inject_path} \;
+
+    # Copy library links to host injection path
+    sudo find ${efa_path} ${openmpi_path} ${pmix_path} -maxdepth 2 -type l -name "*.so*" -exec cp -P {} ${host_injection_mpi_path} \;
+
+    # Get system libefa.so and libibverbs.so
+    find /lib/ /lib64/ \( -name "libefa.so*" -or -name "libibverbs.so*" \) -type f -exec cp {} ${temp_inject_path} \;
+    sudo find /lib/ /lib64/ \( -name "libefa.so*" -or -name "libibverbs.so*" \) -type l -exec cp -P {} ${host_injection_mpi_path} \;
+
+
+    # Get MPI libs dependencies from system ldd
+    local libname libpath
+    local -A libs_arr
+
+    while read -r libname libpath; do
+	[[ ${libpath} =~ ${AMAZON_PATH}/.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
+	[[ ${libname} =~ libefa\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
+	[[ ${libname} =~ libibverbs\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
+	libs_arr[${libname}]=${libpath}
+    done < <(cat <(${system_ldd} ${temp_inject_path}/*) <(find ${openmpi_path} -mindepth 3 -name "*.so*" -print0 | xargs -0 ${system_ldd}) | awk '/=>/{print $1, $3}' | sort | uniq)
+
+    # Get MPI related lib dependencies not resolved by EESSI ldd
+    local lib
+
+    while read -r lib; do
+	local dep
+
+	${PATCHELF_BIN} --set-rpath "" ${lib}
+
+	while read -r dep; do
+	    if ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
+			${PATCHELF_BIN} --replace-needed ${dep} ${libs_arr[${dep}]} ${lib}
+	    fi
+	done < <(${eessi_ldd} ${lib} | awk '/not found/ || /libefa/ || /libibverbs/ {print $1}' | sort | uniq)
+
+	# Inject into libmpi.so non resolved dependencies from dlopen libraries that are not already present in libmpi.so
+	if [[ ${lib} =~ libmpi\.so ]]; then
+	    while read -r dep; do
+			${PATCHELF_BIN} --add-needed ${libs_arr[${dep}]} ${lib}
+	    done < <(comm -23 <(find ${openmpi_path} -mindepth 3 -name "*.so*" -print0 | xargs -0 ${eessi_ldd} | awk '/not found/ {print $1}' | sort | uniq) <(${PATCHELF_BIN} --print-needed ${lib} | sort))
+	fi
+
+    done < <(find ${temp_inject_path} -type f)
+
+    # Sanity check MPI injection
+    if ${eessi_ldd} ${temp_inject_path}/* &> /dev/null; then
+		sudo cp ${temp_inject_path}/* -t ${host_injection_mpi_path}
+		echo_green "MPI injection was successful"
+		return 0
+    else
+		fatal_error "MPI host injection failed. EESSI will use its own MPI libraries"
+    fi
+}
+
+
+main() {
+    process_cmdline "$@"
+    get_os_release
+	check_eessi_initialised
+
+	# we need a directory we can use for temporary storage
+	if [[ -z "${TEMP_DIR}" ]]; then
+		tmpdir=$(mktemp -d)
+	else
+		tmpdir="${TEMP_DIR}"/temp
+		if ! mkdir -p "$tmpdir" ; then
+			fatal_error "Could not create directory ${tmpdir}"
+		fi
+	fi
+
+	echo "OpenMPI version to inject: ${OPENMPI_VERSION}"
+	download_patchelf
+	inject_mpi
+
+    rm -rf "${tmpdir}"
+    echo "EESSI setup completed with success"
+}
+
+main "$@"

From 84f30b1f41d9ba891367377ca9e71159a6072f74 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Mon, 17 Feb 2025 13:00:55 +0100
Subject: [PATCH 02/20] remove tabs

---
 .../install_openmpi_host_injection.sh         | 166 +++++++++---------
 1 file changed, 83 insertions(+), 83 deletions(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 79cc428099..153f385b41 100644
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -20,7 +20,7 @@ show_help() {
     echo "Options:"
     echo "  --help                           Display this help message"
     echo "  --mpi-path /path/to/mpi          Specify the path to the MPI host installation"
-	echo "  --pmix-path /path/to/mpi         Specify the path to the PMIX host installation"
+    echo "  --pmix-path /path/to/mpi         Specify the path to the PMIX host installation"
     echo "  -t, --temp-dir /path/to/tmpdir   Specify a location to use for temporary"
     echo "                                   storage during the mpi injection"
     echo "                                   (must have >10GB available)"
@@ -35,54 +35,54 @@ get_os_release() {
     local value
 
     while read -r key value; do
-	OS_RELEASE[${key}]="${value}"
+    OS_RELEASE[${key}]="${value}"
     done < <(awk -F = 'gsub(/"/, "", $2); {print $1, $2}' /etc/os-release)
 }
 
 
 parse_cmdline() {
-	while [[ $# -gt 0 ]]; do
-		case "$1" in
-			--help)
-				show_help
-				exit 0
-				;;
-			--mpi-path)
-				if [ -n "$2" ]; then
-					MPI_PATH="$2"
-					shift 2
-				else
-					echo "Error: Argument required for $1"
-					show_help
-					exit 1
-				fi
-				;;
-			--pmix-path)
-				if [ -n "$2" ]; then
-					PMIX_PATH="$2"
-					shift 2
-				else
-					echo "Error: Argument required for $1"
-					show_help
-					exit 1
-				fi
-				;;
-			-t|--temp-dir)
-				if [ -n "$2" ]; then
-					TEMP_DIR="$2"
-					shift 2
-				else
-					echo "Error: Argument required for $1"
-					show_help
-					exit 1
-				fi
-				;;
-			*)
-				show_help
-				fatal_error "Error: Unknown option: $1"
-				;;
-		esac
-	done
+    while [[ $# -gt 0 ]]; do
+        case "$1" in
+            --help)
+                show_help
+                exit 0
+                ;;
+            --mpi-path)
+                if [ -n "$2" ]; then
+                    MPI_PATH="$2"
+                    shift 2
+                else
+                    echo "Error: Argument required for $1"
+                    show_help
+                    exit 1
+                fi
+                ;;
+            --pmix-path)
+                if [ -n "$2" ]; then
+                    PMIX_PATH="$2"
+                    shift 2
+                else
+                    echo "Error: Argument required for $1"
+                    show_help
+                    exit 1
+                fi
+                ;;
+            -t|--temp-dir)
+                if [ -n "$2" ]; then
+                    TEMP_DIR="$2"
+                    shift 2
+                else
+                    echo "Error: Argument required for $1"
+                    show_help
+                    exit 1
+                fi
+                ;;
+            *)
+                show_help
+                fatal_error "Error: Unknown option: $1"
+                ;;
+        esac
+    done
 }
 
 
@@ -113,13 +113,13 @@ inject_mpi() {
 
     local host_injection_mpi_path
 
-	host_injection_mpi_path=${EESSI_SOFTWARE_PATH/versions/host_injections}
+    host_injection_mpi_path=${EESSI_SOFTWARE_PATH/versions/host_injections}
     host_injection_mpi_path+="/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}"
     host_injection_mpi_path+="/rpath_overrides/OpenMPI/system/lib"
 
     if [ -d ${host_injection_mpi_path} ]; then
-		echo "MPI was already injected"
-		return 0
+        echo "MPI was already injected"
+        return 0
     fi
 
     sudo mkdir -p ${host_injection_mpi_path}
@@ -143,42 +143,42 @@ inject_mpi() {
     local -A libs_arr
 
     while read -r libname libpath; do
-	[[ ${libpath} =~ ${AMAZON_PATH}/.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
-	[[ ${libname} =~ libefa\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
-	[[ ${libname} =~ libibverbs\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
-	libs_arr[${libname}]=${libpath}
+    [[ ${libpath} =~ ${AMAZON_PATH}/.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
+    [[ ${libname} =~ libefa\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
+    [[ ${libname} =~ libibverbs\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
+    libs_arr[${libname}]=${libpath}
     done < <(cat <(${system_ldd} ${temp_inject_path}/*) <(find ${openmpi_path} -mindepth 3 -name "*.so*" -print0 | xargs -0 ${system_ldd}) | awk '/=>/{print $1, $3}' | sort | uniq)
 
     # Get MPI related lib dependencies not resolved by EESSI ldd
     local lib
 
     while read -r lib; do
-	local dep
+    local dep
 
-	${PATCHELF_BIN} --set-rpath "" ${lib}
+    ${PATCHELF_BIN} --set-rpath "" ${lib}
 
-	while read -r dep; do
-	    if ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
-			${PATCHELF_BIN} --replace-needed ${dep} ${libs_arr[${dep}]} ${lib}
-	    fi
-	done < <(${eessi_ldd} ${lib} | awk '/not found/ || /libefa/ || /libibverbs/ {print $1}' | sort | uniq)
+    while read -r dep; do
+        if ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
+            ${PATCHELF_BIN} --replace-needed ${dep} ${libs_arr[${dep}]} ${lib}
+        fi
+    done < <(${eessi_ldd} ${lib} | awk '/not found/ || /libefa/ || /libibverbs/ {print $1}' | sort | uniq)
 
-	# Inject into libmpi.so non resolved dependencies from dlopen libraries that are not already present in libmpi.so
-	if [[ ${lib} =~ libmpi\.so ]]; then
-	    while read -r dep; do
-			${PATCHELF_BIN} --add-needed ${libs_arr[${dep}]} ${lib}
-	    done < <(comm -23 <(find ${openmpi_path} -mindepth 3 -name "*.so*" -print0 | xargs -0 ${eessi_ldd} | awk '/not found/ {print $1}' | sort | uniq) <(${PATCHELF_BIN} --print-needed ${lib} | sort))
-	fi
+    # Inject into libmpi.so non resolved dependencies from dlopen libraries that are not already present in libmpi.so
+    if [[ ${lib} =~ libmpi\.so ]]; then
+        while read -r dep; do
+            ${PATCHELF_BIN} --add-needed ${libs_arr[${dep}]} ${lib}
+        done < <(comm -23 <(find ${openmpi_path} -mindepth 3 -name "*.so*" -print0 | xargs -0 ${eessi_ldd} | awk '/not found/ {print $1}' | sort | uniq) <(${PATCHELF_BIN} --print-needed ${lib} | sort))
+    fi
 
     done < <(find ${temp_inject_path} -type f)
 
     # Sanity check MPI injection
     if ${eessi_ldd} ${temp_inject_path}/* &> /dev/null; then
-		sudo cp ${temp_inject_path}/* -t ${host_injection_mpi_path}
-		echo_green "MPI injection was successful"
-		return 0
+        sudo cp ${temp_inject_path}/* -t ${host_injection_mpi_path}
+        echo_green "MPI injection was successful"
+        return 0
     else
-		fatal_error "MPI host injection failed. EESSI will use its own MPI libraries"
+        fatal_error "MPI host injection failed. EESSI will use its own MPI libraries"
     fi
 }
 
@@ -186,21 +186,21 @@ inject_mpi() {
 main() {
     process_cmdline "$@"
     get_os_release
-	check_eessi_initialised
-
-	# we need a directory we can use for temporary storage
-	if [[ -z "${TEMP_DIR}" ]]; then
-		tmpdir=$(mktemp -d)
-	else
-		tmpdir="${TEMP_DIR}"/temp
-		if ! mkdir -p "$tmpdir" ; then
-			fatal_error "Could not create directory ${tmpdir}"
-		fi
-	fi
-
-	echo "OpenMPI version to inject: ${OPENMPI_VERSION}"
-	download_patchelf
-	inject_mpi
+    check_eessi_initialised
+
+    # we need a directory we can use for temporary storage
+    if [[ -z "${TEMP_DIR}" ]]; then
+        tmpdir=$(mktemp -d)
+    else
+        tmpdir="${TEMP_DIR}"/temp
+        if ! mkdir -p "$tmpdir" ; then
+            fatal_error "Could not create directory ${tmpdir}"
+        fi
+    fi
+
+    echo "OpenMPI version to inject: ${OPENMPI_VERSION}"
+    download_patchelf
+    inject_mpi
 
     rm -rf "${tmpdir}"
     echo "EESSI setup completed with success"

From 3851e0167cae250461a6a2a3dec3dc7a91355799 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Mon, 17 Feb 2025 13:23:24 +0100
Subject: [PATCH 03/20] fix indentation

---
 scripts/mpi_support/install_openmpi_host_injection.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 153f385b41..cddc53cb51 100644
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -143,10 +143,10 @@ inject_mpi() {
     local -A libs_arr
 
     while read -r libname libpath; do
-    [[ ${libpath} =~ ${AMAZON_PATH}/.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
-    [[ ${libname} =~ libefa\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
-    [[ ${libname} =~ libibverbs\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
-    libs_arr[${libname}]=${libpath}
+        [[ ${libpath} =~ ${AMAZON_PATH}/.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
+        [[ ${libname} =~ libefa\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
+        [[ ${libname} =~ libibverbs\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
+        libs_arr[${libname}]=${libpath}
     done < <(cat <(${system_ldd} ${temp_inject_path}/*) <(find ${openmpi_path} -mindepth 3 -name "*.so*" -print0 | xargs -0 ${system_ldd}) | awk '/=>/{print $1, $3}' | sort | uniq)
 
     # Get MPI related lib dependencies not resolved by EESSI ldd

From 95f917dfa58d4ef392dab576b1540b50b08aeaed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Mon, 17 Feb 2025 16:34:49 +0100
Subject: [PATCH 04/20] fix indentation

---
 .../install_openmpi_host_injection.sh         | 26 +++++++++----------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index cddc53cb51..ab45e8d0a6 100644
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -153,22 +153,22 @@ inject_mpi() {
     local lib
 
     while read -r lib; do
-    local dep
+        local dep
 
-    ${PATCHELF_BIN} --set-rpath "" ${lib}
+        ${PATCHELF_BIN} --set-rpath "" ${lib}
 
-    while read -r dep; do
-        if ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
-            ${PATCHELF_BIN} --replace-needed ${dep} ${libs_arr[${dep}]} ${lib}
-        fi
-    done < <(${eessi_ldd} ${lib} | awk '/not found/ || /libefa/ || /libibverbs/ {print $1}' | sort | uniq)
-
-    # Inject into libmpi.so non resolved dependencies from dlopen libraries that are not already present in libmpi.so
-    if [[ ${lib} =~ libmpi\.so ]]; then
         while read -r dep; do
-            ${PATCHELF_BIN} --add-needed ${libs_arr[${dep}]} ${lib}
-        done < <(comm -23 <(find ${openmpi_path} -mindepth 3 -name "*.so*" -print0 | xargs -0 ${eessi_ldd} | awk '/not found/ {print $1}' | sort | uniq) <(${PATCHELF_BIN} --print-needed ${lib} | sort))
-    fi
+            if ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
+                ${PATCHELF_BIN} --replace-needed ${dep} ${libs_arr[${dep}]} ${lib}
+            fi
+        done < <(${eessi_ldd} ${lib} | awk '/not found/ || /libefa/ || /libibverbs/ {print $1}' | sort | uniq)
+
+        # Inject into libmpi.so non resolved dependencies from dlopen libraries that are not already present in libmpi.so
+        if [[ ${lib} =~ libmpi\.so ]]; then
+            while read -r dep; do
+                ${PATCHELF_BIN} --add-needed ${libs_arr[${dep}]} ${lib}
+            done < <(comm -23 <(find ${openmpi_path} -mindepth 3 -name "*.so*" -print0 | xargs -0 ${eessi_ldd} | awk '/not found/ {print $1}' | sort | uniq) <(${PATCHELF_BIN} --print-needed ${lib} | sort))
+        fi
 
     done < <(find ${temp_inject_path} -type f)
 

From 4251a12993f5212f733318f306c11f2138889c18 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Thu, 27 Feb 2025 19:42:12 +0100
Subject: [PATCH 05/20] generalize script

---
 .../install_openmpi_host_injection.sh         | 164 ++++++++++--------
 1 file changed, 89 insertions(+), 75 deletions(-)
 mode change 100644 => 100755 scripts/mpi_support/install_openmpi_host_injection.sh

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
old mode 100644
new mode 100755
index ab45e8d0a6..7c38d05339
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -11,7 +11,7 @@
 
 # Initialise our bash functions
 TOPDIR=$(dirname $(realpath $BASH_SOURCE))
-source "$TOPDIR"/../../utils.sh
+source "$TOPDIR"/../utils.sh
 
 
 # Function to display help message
@@ -19,24 +19,10 @@ show_help() {
     echo "Usage: $0 [OPTIONS]"
     echo "Options:"
     echo "  --help                           Display this help message"
-    echo "  --mpi-path /path/to/mpi          Specify the path to the MPI host installation"
-    echo "  --pmix-path /path/to/mpi         Specify the path to the PMIX host installation"
+    echo "  --mpi-path /path/to/mpi          Specify the path to the MPI host installation (Required)"
     echo "  -t, --temp-dir /path/to/tmpdir   Specify a location to use for temporary"
     echo "                                   storage during the mpi injection"
-    echo "                                   (must have >10GB available)"
-}
-
-
-# Global associative array with os-release info
-declare -A OS_RELEASE
-
-get_os_release() {
-    local key
-    local value
-
-    while read -r key value; do
-    OS_RELEASE[${key}]="${value}"
-    done < <(awk -F = 'gsub(/"/, "", $2); {print $1, $2}' /etc/os-release)
+    echo "  --noclean                        Do not remove the temporary directory after finishing injection"
 }
 
 
@@ -49,68 +35,73 @@ parse_cmdline() {
                 ;;
             --mpi-path)
                 if [ -n "$2" ]; then
-                    MPI_PATH="$2"
+                    readonly MPI_PATH="$2"
                     shift 2
                 else
-                    echo "Error: Argument required for $1"
-                    show_help
-                    exit 1
-                fi
-                ;;
-            --pmix-path)
-                if [ -n "$2" ]; then
-                    PMIX_PATH="$2"
-                    shift 2
-                else
-                    echo "Error: Argument required for $1"
+                    echo_red "Error: Argument required for $1"
                     show_help
                     exit 1
                 fi
                 ;;
             -t|--temp-dir)
                 if [ -n "$2" ]; then
-                    TEMP_DIR="$2"
+                    readonly TEMP_DIR="$2"
                     shift 2
                 else
-                    echo "Error: Argument required for $1"
+                    echo_red "Error: Argument required for $1"
                     show_help
                     exit 1
                 fi
                 ;;
+            --noclean)
+                CLEAN=false
+                shift 1
+                ;;
             *)
+                echo_red "Error: Unknown option: $1"
                 show_help
-                fatal_error "Error: Unknown option: $1"
+                exit 1
                 ;;
         esac
     done
+    if [ -z "${MPI_PATH}" ]; then
+        echo_yellow "MPI path was not specified and it is required"
+        show_help
+        exit 0
+    fi
+    readonly CLEAN=${CLEAN:=true}
 }
 
 
 # ****Warning: patchelf v0.18.0 (currently shipped with EESSI) does not work.****
 # We get v0.17.2
 download_patchelf() {
+    # Temporary directory to save patchelf
+    local tmpdir=$1
+
     local patchelf_version="0.17.2"
     local url
+    local curl_opts="-L --silent --show-error --fail"
 
     url="https://github.com/NixOS/patchelf/releases/download/${patchelf_version}/"
     url+="patchelf-${patchelf_version}-${EESSI_CPU_FAMILY}.tar.gz"
 
-    curl ${url} ${CURL_OPTS} -o ${TEMP_DIR}/patchelf.tar.gz
-    tar -xf ${TEMP_DIR}/patchelf.tar.gz -C ${TEMP_DIR}
-    PATCHELF_BIN=${TEMP_DIR}/bin/patchelf
+    local patchelf_path=${tmpdir}/patchelf
+    mkdir ${patchelf_path}
+
+    curl ${url} ${curl_opts} -o ${patchelf_path}/patchelf.tar.gz
+    tar -xf ${patchelf_path}/patchelf.tar.gz -C ${patchelf_path}
+    PATCHELF_BIN=${patchelf_path}/bin/patchelf
 }
 
 
 inject_mpi() {
-    local efa_path="${AMAZON_PATH}/efa"
-    local openmpi_path="${MPI_PATH}"
-    local pmix_path="${PMIX_PATH}"
+    # Temporary directory for injection
+    local tmpdir=$1
 
     local eessi_ldd="${EESSI_EPREFIX}/usr/bin/ldd"
     local system_ldd="/usr/bin/ldd"
 
-    (( OPENMPI_VERSION == 5 )) && openmpi_path+=5
-
     local host_injection_mpi_path
 
     host_injection_mpi_path=${EESSI_SOFTWARE_PATH/versions/host_injections}
@@ -118,63 +109,81 @@ inject_mpi() {
     host_injection_mpi_path+="/rpath_overrides/OpenMPI/system/lib"
 
     if [ -d ${host_injection_mpi_path} ]; then
-        echo "MPI was already injected"
-        return 0
+        if [ -n "$(ls -A ${host_injection_mpi_path})" ]; then
+            echo "MPI was already injected"
+            return 0
+        fi
     fi
 
-    sudo mkdir -p ${host_injection_mpi_path}
+    mkdir -p ${host_injection_mpi_path}
 
-    local temp_inject_path="${TEMP_DIR}/mpi_inject"
+    local temp_inject_path="${tmpdir}/mpi_inject"
     mkdir ${temp_inject_path}
 
-    # Get all library files from efa and openmpi dirs
-    find ${efa_path} ${openmpi_path} ${pmix_path} -maxdepth 2 -type f -name "*.so*" -exec cp {} ${temp_inject_path} \;
+    # Get all library files from openmpi dir
+    find ${MPI_PATH} -maxdepth 1 -type f -name "*.so*" -exec cp {} ${temp_inject_path} \;
 
     # Copy library links to host injection path
-    sudo find ${efa_path} ${openmpi_path} ${pmix_path} -maxdepth 2 -type l -name "*.so*" -exec cp -P {} ${host_injection_mpi_path} \;
-
-    # Get system libefa.so and libibverbs.so
-    find /lib/ /lib64/ \( -name "libefa.so*" -or -name "libibverbs.so*" \) -type f -exec cp {} ${temp_inject_path} \;
-    sudo find /lib/ /lib64/ \( -name "libefa.so*" -or -name "libibverbs.so*" \) -type l -exec cp -P {} ${host_injection_mpi_path} \;
-
+    find ${MPI_PATH} -maxdepth 1 -type l -name "*.so*" -exec cp -P {} ${host_injection_mpi_path} \;
 
     # Get MPI libs dependencies from system ldd
     local libname libpath
-    local -A libs_arr
+    local -A libs_dict
+    local -a dlopen_libs
+
+    readarray -d '' dlopen_libs < <(find ${MPI_PATH} -mindepth 2 -name "*.so*")
 
+    # Get all library names and paths in associative array
     while read -r libname libpath; do
-        [[ ${libpath} =~ ${AMAZON_PATH}/.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
-        [[ ${libname} =~ libefa\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
-        [[ ${libname} =~ libibverbs\.so\.?.* ]] && libpath=${host_injection_mpi_path}/$(basename ${libpath})
-        libs_arr[${libname}]=${libpath}
-    done < <(cat <(${system_ldd} ${temp_inject_path}/*) <(find ${openmpi_path} -mindepth 3 -name "*.so*" -print0 | xargs -0 ${system_ldd}) | awk '/=>/{print $1, $3}' | sort | uniq)
+        # If library is libfabric or from the MPI path, modify libpath in assoc array to point to host_injection_mpi_path
+        if [[ ${libname} =~ libfabric\.so\.?.* ]] && [[ ! -f ${temp_inject_path}/${libname} ]]; then
+            local libdir="$(dirname ${libpath})/"     # without trailing slash the find does not work
+            find ${libdir} -maxdepth 1 -type f -name "libfabric.so*" -exec cp {} ${temp_inject_path} \;
+            find ${libdir} -maxdepth 1 -type l -name "libfabric.so*" -exec cp -P {} ${host_injection_mpi_path} \;
+            libpath=${host_injection_mpi_path}/$(basename ${libpath})
+        fi
+
+        if [[ ${libpath} =~ ${MPI_PATH}/.* ]]; then
+            libpath=${host_injection_mpi_path}/$(basename ${libpath})
+        fi
+        
+        libs_dict[${libname}]=${libpath}
+    done < <(cat <(find ${temp_inject_path} -maxdepth 1 -type f -name "*.so*" -exec ${system_ldd} {} \;) \
+                 <(for dlopen in ${dlopen_libs[@]}; do ${system_ldd} ${dlopen}; done) \
+            | awk '/=>/ {print $1, $3}' | sort | uniq)
 
     # Get MPI related lib dependencies not resolved by EESSI ldd
     local lib
-
     while read -r lib; do
         local dep
 
-        ${PATCHELF_BIN} --set-rpath "" ${lib}
-
+        ${PATCHELF_BIN} --set-rpath "${host_injection_mpi_path}" ${lib}
         while read -r dep; do
-            if ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
-                ${PATCHELF_BIN} --replace-needed ${dep} ${libs_arr[${dep}]} ${lib}
-            fi
-        done < <(${eessi_ldd} ${lib} | awk '/not found/ || /libefa/ || /libibverbs/ {print $1}' | sort | uniq)
+            ${PATCHELF_BIN} --replace-needed ${dep} ${libs_dict[${dep}]} ${lib}
+        done < <(${eessi_ldd} ${lib} | awk '/not found/ {print $1}' | sort | uniq)
 
         # Inject into libmpi.so non resolved dependencies from dlopen libraries that are not already present in libmpi.so
         if [[ ${lib} =~ libmpi\.so ]]; then
             while read -r dep; do
-                ${PATCHELF_BIN} --add-needed ${libs_arr[${dep}]} ${lib}
-            done < <(comm -23 <(find ${openmpi_path} -mindepth 3 -name "*.so*" -print0 | xargs -0 ${eessi_ldd} | awk '/not found/ {print $1}' | sort | uniq) <(${PATCHELF_BIN} --print-needed ${lib} | sort))
+                if ! ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
+                    ${PATCHELF_BIN} --add-needed ${libs_dict[${dep}]} ${lib}                    
+                fi
+            done < <(for dlopen in ${dlopen_libs[@]}; do ${eessi_ldd} ${dlopen}; done \
+                     | grep -e "=> not found" -e "=> ${MPI_PATH}" | awk '{print $1}' | sort | uniq)
+        fi
+
+        # Force system libefa, librdmacm, libibverbs and libpsm2 (present in the EESSI compat layer)
+        if [[ ${lib} =~ libfabric\.so\.?.* ]]; then
+            while read -r dep; do
+                ${PATCHELF_BIN} --replace-needed ${dep} ${libs_dict[${dep}]} ${lib}
+            done < <(${system_ldd} ${lib} | awk '/libefa/ || /libibverbs/ || /libpsm2/ || /librdmacm/ {print $1}' | sort | uniq)
         fi
 
     done < <(find ${temp_inject_path} -type f)
 
     # Sanity check MPI injection
     if ${eessi_ldd} ${temp_inject_path}/* &> /dev/null; then
-        sudo cp ${temp_inject_path}/* -t ${host_injection_mpi_path}
+        cp ${temp_inject_path}/* -t ${host_injection_mpi_path}
         echo_green "MPI injection was successful"
         return 0
     else
@@ -184,10 +193,13 @@ inject_mpi() {
 
 
 main() {
-    process_cmdline "$@"
-    get_os_release
+    parse_cmdline "$@"
     check_eessi_initialised
 
+    # Create directory linked by host_injections
+    local inject_dir=$(readlink -f /cvmfs/software.eessi.io/host_injections)
+    [[ ! -d ${inject_dir} ]] && mkdir -p ${inject_dir}
+
     # we need a directory we can use for temporary storage
     if [[ -z "${TEMP_DIR}" ]]; then
         tmpdir=$(mktemp -d)
@@ -198,12 +210,14 @@ main() {
         fi
     fi
 
-    echo "OpenMPI version to inject: ${OPENMPI_VERSION}"
-    download_patchelf
-    inject_mpi
+    echo "Temporary directory for injection: ${tmpdir}"
 
-    rm -rf "${tmpdir}"
-    echo "EESSI setup completed with success"
+    download_patchelf ${tmpdir}
+    inject_mpi ${tmpdir}
+
+    if ${CLEAN}; then
+        rm -rf "${tmpdir}"
+    fi
 }
 
 main "$@"

From 4c89f2cd5e3823902ae7d2fa2570ca8dac0d55a0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Fri, 28 Feb 2025 17:55:58 +0100
Subject: [PATCH 06/20] add to libmpi only not found libs in dlopen libraries

---
 scripts/mpi_support/install_openmpi_host_injection.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 7c38d05339..035d8d739a 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -168,8 +168,7 @@ inject_mpi() {
                 if ! ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
                     ${PATCHELF_BIN} --add-needed ${libs_dict[${dep}]} ${lib}                    
                 fi
-            done < <(for dlopen in ${dlopen_libs[@]}; do ${eessi_ldd} ${dlopen}; done \
-                     | grep -e "=> not found" -e "=> ${MPI_PATH}" | awk '{print $1}' | sort | uniq)
+            done < <(for dlopen in ${dlopen_libs[@]}; do ${eessi_ldd} ${dlopen}; done | awk '/not found/ {print $1}' | sort | uniq)
         fi
 
         # Force system libefa, librdmacm, libibverbs and libpsm2 (present in the EESSI compat layer)

From e9efd6e6c7747624acfc11de2750f13e3b18db92 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Mon, 3 Mar 2025 12:47:04 +0100
Subject: [PATCH 07/20] fix mpi injection path

---
 scripts/mpi_support/install_openmpi_host_injection.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 035d8d739a..96158a409a 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -105,7 +105,6 @@ inject_mpi() {
     local host_injection_mpi_path
 
     host_injection_mpi_path=${EESSI_SOFTWARE_PATH/versions/host_injections}
-    host_injection_mpi_path+="/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}"
     host_injection_mpi_path+="/rpath_overrides/OpenMPI/system/lib"
 
     if [ -d ${host_injection_mpi_path} ]; then

From 9c067d8d1aa4d3db5e87126804d8141c1d1967bb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Mon, 3 Mar 2025 16:20:31 +0100
Subject: [PATCH 08/20] inject the libpmix library

---
 scripts/mpi_support/install_openmpi_host_injection.sh | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 96158a409a..45b1bef8eb 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -142,11 +142,19 @@ inject_mpi() {
             libpath=${host_injection_mpi_path}/$(basename ${libpath})
         fi
 
+        if [[ ${libname} =~ libpmix\.so\.?.* ]] && [[ ! -f ${temp_inject_path}/${libname} ]]; then
+            local libdir="$(dirname ${libpath})/"     # without trailing slash the find does not work
+            find ${libdir} -maxdepth 1 -type f -name "libpmix.so*" -exec cp {} ${temp_inject_path} \;
+            find ${libdir} -maxdepth 1 -type l -name "libpmix.so*" -exec cp -P {} ${host_injection_mpi_path} \;
+            libpath=${host_injection_mpi_path}/$(basename ${libpath})
+        fi
+
         if [[ ${libpath} =~ ${MPI_PATH}/.* ]]; then
             libpath=${host_injection_mpi_path}/$(basename ${libpath})
         fi
         
         libs_dict[${libname}]=${libpath}
+
     done < <(cat <(find ${temp_inject_path} -maxdepth 1 -type f -name "*.so*" -exec ${system_ldd} {} \;) \
                  <(for dlopen in ${dlopen_libs[@]}; do ${system_ldd} ${dlopen}; done) \
             | awk '/=>/ {print $1, $3}' | sort | uniq)

From 1dca91178d92b052c1b0c10847ecf5b905218300 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Mon, 3 Mar 2025 18:40:51 +0100
Subject: [PATCH 09/20] revert to inject dependencies from dlopen libs in mpi
 path

---
 scripts/mpi_support/install_openmpi_host_injection.sh | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 45b1bef8eb..560ffec5e0 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -149,7 +149,7 @@ inject_mpi() {
             libpath=${host_injection_mpi_path}/$(basename ${libpath})
         fi
 
-        if [[ ${libpath} =~ ${MPI_PATH}/.* ]]; then
+        if [[ ${libpath} =~ ${MPI_PATH} ]]; then
             libpath=${host_injection_mpi_path}/$(basename ${libpath})
         fi
         
@@ -173,9 +173,11 @@ inject_mpi() {
         if [[ ${lib} =~ libmpi\.so ]]; then
             while read -r dep; do
                 if ! ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
-                    ${PATCHELF_BIN} --add-needed ${libs_dict[${dep}]} ${lib}                    
+                    ${PATCHELF_BIN} --add-needed ${libs_dict[${dep}]} ${lib}
                 fi
-            done < <(for dlopen in ${dlopen_libs[@]}; do ${eessi_ldd} ${dlopen}; done | awk '/not found/ {print $1}' | sort | uniq)
+            done < <(for dlopen in ${dlopen_libs[@]}; do ${eessi_ldd} ${dlopen}; done \
+                     | grep -e "=> not found" -e "=> ${MPI_PATH}" | awk '!/libmpi\.so.*/ {print $1}' | sort | uniq)
+        fi
         fi
 
         # Force system libefa, librdmacm, libibverbs and libpsm2 (present in the EESSI compat layer)

From 0cf08c541ef241ff35940702079417e87f9bff8f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Mon, 3 Mar 2025 18:41:15 +0100
Subject: [PATCH 10/20] add pmix injection

---
 .../install_openmpi_host_injection.sh         | 33 ++++++++++++++++++-
 1 file changed, 32 insertions(+), 1 deletion(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 560ffec5e0..7b031b461e 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -43,6 +43,16 @@ parse_cmdline() {
                     exit 1
                 fi
                 ;;
+            --pmix-path)
+                if [ -n "$2"]; then
+                    readonly PMIX_PATH="$2"
+                    shift 2
+                else
+                    echo_red "Error: Argument required for $1"
+                    show_help
+                    exit 1
+                fi
+                ;;
             -t|--temp-dir)
                 if [ -n "$2" ]; then
                     readonly TEMP_DIR="$2"
@@ -69,6 +79,12 @@ parse_cmdline() {
         show_help
         exit 0
     fi
+
+    if [ -z "${PMIX_PATH}" ]; then
+        echo_yellow "PMIX path was not specified"
+        echo_yellow "Assuming it is the directory where libpmix is found"
+    fi
+
     readonly CLEAN=${CLEAN:=true}
 }
 
@@ -126,7 +142,7 @@ inject_mpi() {
     find ${MPI_PATH} -maxdepth 1 -type l -name "*.so*" -exec cp -P {} ${host_injection_mpi_path} \;
 
     # Get MPI libs dependencies from system ldd
-    local libname libpath
+    local libname libpath pmixpath
     local -A libs_dict
     local -a dlopen_libs
 
@@ -144,8 +160,15 @@ inject_mpi() {
 
         if [[ ${libname} =~ libpmix\.so\.?.* ]] && [[ ! -f ${temp_inject_path}/${libname} ]]; then
             local libdir="$(dirname ${libpath})/"     # without trailing slash the find does not work
+            [ -n "${PMIX_PATH}" ] && pmixpath="${PMIX_PATH}/pmix" || pmixpath="$(dirname ${libpath})/pmix"
             find ${libdir} -maxdepth 1 -type f -name "libpmix.so*" -exec cp {} ${temp_inject_path} \;
             find ${libdir} -maxdepth 1 -type l -name "libpmix.so*" -exec cp -P {} ${host_injection_mpi_path} \;
+
+            local depname deppath
+            while read -r depname deppath; do
+                libs_dict[${depname}]=${deppath}
+            done < <(find ${pmixpath} -maxdepth 1 -name "*.so*" -exec ${system_ldd} {} \; | awk '/=>/ {print $1, $3}' | sort | uniq)
+
             libpath=${host_injection_mpi_path}/$(basename ${libpath})
         fi
 
@@ -178,6 +201,14 @@ inject_mpi() {
             done < <(for dlopen in ${dlopen_libs[@]}; do ${eessi_ldd} ${dlopen}; done \
                      | grep -e "=> not found" -e "=> ${MPI_PATH}" | awk '!/libmpi\.so.*/ {print $1}' | sort | uniq)
         fi
+
+        # Inject into libpmix.so non resolved dependencies from dlopen libraries in the PMIX path
+        if [[ ${lib} =~ libpmix\.so ]]; then            
+            while read -r dep; do
+                if ! ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
+                    ${PATCHELF_BIN} --add-needed ${libs_dict[${dep}]} ${lib}
+                fi
+            done < <(find ${pmixpath} -maxdepth 1 -type f -name "*.so*" -exec ${eessi_ldd} {} \; | awk '/not found/ && !/libpmix\.so.*/ {print $1}' | sort | uniq)
         fi
 
         # Force system libefa, librdmacm, libibverbs and libpsm2 (present in the EESSI compat layer)

From 2d0373b6439cda5075690393bf88a76c97896a01 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Mon, 3 Mar 2025 19:12:57 +0100
Subject: [PATCH 11/20] add libfabric dependencies to the libs dictionary

---
 scripts/mpi_support/install_openmpi_host_injection.sh | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 7b031b461e..ceace8c805 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -155,6 +155,12 @@ inject_mpi() {
             local libdir="$(dirname ${libpath})/"     # without trailing slash the find does not work
             find ${libdir} -maxdepth 1 -type f -name "libfabric.so*" -exec cp {} ${temp_inject_path} \;
             find ${libdir} -maxdepth 1 -type l -name "libfabric.so*" -exec cp -P {} ${host_injection_mpi_path} \;
+
+            local depname deppath
+            while read -r depname deppath; do
+                libs_dict[${depname}]=${deppath}
+            done < <(${system_ldd} ${libpath} | awk '/=>/ {print $1, $3}' | sort | uniq)
+
             libpath=${host_injection_mpi_path}/$(basename ${libpath})
         fi
 

From bcf8d135fba102958d2498d012ce79278803f778 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Tue, 4 Mar 2025 10:49:11 +0100
Subject: [PATCH 12/20] simplify regex

---
 scripts/mpi_support/install_openmpi_host_injection.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index ceace8c805..a9ed73ed64 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -151,7 +151,7 @@ inject_mpi() {
     # Get all library names and paths in associative array
     while read -r libname libpath; do
         # If library is libfabric or from the MPI path, modify libpath in assoc array to point to host_injection_mpi_path
-        if [[ ${libname} =~ libfabric\.so\.?.* ]] && [[ ! -f ${temp_inject_path}/${libname} ]]; then
+        if [[ ${libname} =~ libfabric\.so ]] && [[ ! -f ${temp_inject_path}/${libname} ]]; then
             local libdir="$(dirname ${libpath})/"     # without trailing slash the find does not work
             find ${libdir} -maxdepth 1 -type f -name "libfabric.so*" -exec cp {} ${temp_inject_path} \;
             find ${libdir} -maxdepth 1 -type l -name "libfabric.so*" -exec cp -P {} ${host_injection_mpi_path} \;
@@ -164,7 +164,7 @@ inject_mpi() {
             libpath=${host_injection_mpi_path}/$(basename ${libpath})
         fi
 
-        if [[ ${libname} =~ libpmix\.so\.?.* ]] && [[ ! -f ${temp_inject_path}/${libname} ]]; then
+        if [[ ${libname} =~ libpmix\.so ]] && [[ ! -f ${temp_inject_path}/${libname} ]]; then
             local libdir="$(dirname ${libpath})/"     # without trailing slash the find does not work
             [ -n "${PMIX_PATH}" ] && pmixpath="${PMIX_PATH}/pmix" || pmixpath="$(dirname ${libpath})/pmix"
             find ${libdir} -maxdepth 1 -type f -name "libpmix.so*" -exec cp {} ${temp_inject_path} \;
@@ -218,7 +218,7 @@ inject_mpi() {
         fi
 
         # Force system libefa, librdmacm, libibverbs and libpsm2 (present in the EESSI compat layer)
-        if [[ ${lib} =~ libfabric\.so\.?.* ]]; then
+        if [[ ${lib} =~ libfabric\.so ]]; then
             while read -r dep; do
                 ${PATCHELF_BIN} --replace-needed ${dep} ${libs_dict[${dep}]} ${lib}
             done < <(${system_ldd} ${lib} | awk '/libefa/ || /libibverbs/ || /libpsm2/ || /librdmacm/ {print $1}' | sort | uniq)

From 18b39fb13963c22559262e3e8ef62005244f42fd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Tue, 4 Mar 2025 12:34:33 +0100
Subject: [PATCH 13/20] update comments

---
 scripts/mpi_support/install_openmpi_host_injection.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index a9ed73ed64..01783fb20b 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -149,8 +149,9 @@ inject_mpi() {
     readarray -d '' dlopen_libs < <(find ${MPI_PATH} -mindepth 2 -name "*.so*")
 
     # Get all library names and paths in associative array
+    # If library is libfabric, libpmix, or from the MPI path
+    # modify libpath in assoc array to point to host_injection_mpi_path
     while read -r libname libpath; do
-        # If library is libfabric or from the MPI path, modify libpath in assoc array to point to host_injection_mpi_path
         if [[ ${libname} =~ libfabric\.so ]] && [[ ! -f ${temp_inject_path}/${libname} ]]; then
             local libdir="$(dirname ${libpath})/"     # without trailing slash the find does not work
             find ${libdir} -maxdepth 1 -type f -name "libfabric.so*" -exec cp {} ${temp_inject_path} \;
@@ -188,7 +189,7 @@ inject_mpi() {
                  <(for dlopen in ${dlopen_libs[@]}; do ${system_ldd} ${dlopen}; done) \
             | awk '/=>/ {print $1, $3}' | sort | uniq)
 
-    # Get MPI related lib dependencies not resolved by EESSI ldd
+    # Do library injection to openmpi libs, libfabric and libpmix
     local lib
     while read -r lib; do
         local dep

From b1983f4ea890947df92947b60cd5aa92e94b5f33 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Tue, 4 Mar 2025 12:37:28 +0100
Subject: [PATCH 14/20] force certain dependencies into libfabric done first

---
 .../install_openmpi_host_injection.sh            | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 01783fb20b..95b6cdcc52 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -194,6 +194,15 @@ inject_mpi() {
     while read -r lib; do
         local dep
 
+        # Force system libefa, librdmacm, libibverbs and libpsm2 (present in the EESSI compat layer)
+        # Must be done before the injection of unresolved dependencies
+        if [[ ${lib} =~ libfabric\.so ]]; then
+            while read -r dep; do
+                ${PATCHELF_BIN} --replace-needed ${dep} ${libs_dict[${dep}]} ${lib}
+            done < <(${system_ldd} ${lib} | awk '/libefa/ || /libibverbs/ || /libpsm2/ || /librdmacm/ {print $1}' | sort | uniq)
+        fi
+
+        # Do injection of unresolved libraries
         ${PATCHELF_BIN} --set-rpath "${host_injection_mpi_path}" ${lib}
         while read -r dep; do
             ${PATCHELF_BIN} --replace-needed ${dep} ${libs_dict[${dep}]} ${lib}
@@ -218,13 +227,6 @@ inject_mpi() {
             done < <(find ${pmixpath} -maxdepth 1 -type f -name "*.so*" -exec ${eessi_ldd} {} \; | awk '/not found/ && !/libpmix\.so.*/ {print $1}' | sort | uniq)
         fi
 
-        # Force system libefa, librdmacm, libibverbs and libpsm2 (present in the EESSI compat layer)
-        if [[ ${lib} =~ libfabric\.so ]]; then
-            while read -r dep; do
-                ${PATCHELF_BIN} --replace-needed ${dep} ${libs_dict[${dep}]} ${lib}
-            done < <(${system_ldd} ${lib} | awk '/libefa/ || /libibverbs/ || /libpsm2/ || /librdmacm/ {print $1}' | sort | uniq)
-        fi
-
     done < <(find ${temp_inject_path} -type f)
 
     # Sanity check MPI injection

From 5deaab100111d2059e630b6404db4af46376ddb2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Tue, 4 Mar 2025 12:45:48 +0100
Subject: [PATCH 15/20] check if unresolved dependency is needed and choose add
 or replace

---
 scripts/mpi_support/install_openmpi_host_injection.sh | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 95b6cdcc52..7a521ad1fa 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -205,7 +205,11 @@ inject_mpi() {
         # Do injection of unresolved libraries
         ${PATCHELF_BIN} --set-rpath "${host_injection_mpi_path}" ${lib}
         while read -r dep; do
-            ${PATCHELF_BIN} --replace-needed ${dep} ${libs_dict[${dep}]} ${lib}
+            if ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
+                ${PATCHELF_BIN} --replace-needed ${dep} ${libs_dict[${dep}]} ${lib}
+            else
+                ${PATCHELF_BIN} --add-needed ${dep} ${libs_dict[${dep}]} ${lib}
+            fi
         done < <(${eessi_ldd} ${lib} | awk '/not found/ {print $1}' | sort | uniq)
 
         # Inject into libmpi.so non resolved dependencies from dlopen libraries that are not already present in libmpi.so

From 3fdbd0b02a8c86f36a3ca6b8b8e602f9f4e13e4d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Tue, 4 Mar 2025 12:47:54 +0100
Subject: [PATCH 16/20] fix add new needed library: only two args needed

---
 scripts/mpi_support/install_openmpi_host_injection.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 7a521ad1fa..6b48b0ac04 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -208,7 +208,7 @@ inject_mpi() {
             if ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
                 ${PATCHELF_BIN} --replace-needed ${dep} ${libs_dict[${dep}]} ${lib}
             else
-                ${PATCHELF_BIN} --add-needed ${dep} ${libs_dict[${dep}]} ${lib}
+                ${PATCHELF_BIN} --add-needed ${libs_dict[${dep}]} ${lib}
             fi
         done < <(${eessi_ldd} ${lib} | awk '/not found/ {print $1}' | sort | uniq)
 

From 883593564ced83a1286fee0b65d15974c2098481 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Tue, 4 Mar 2025 14:05:50 +0100
Subject: [PATCH 17/20] remove unneeded pmix code

---
 .../install_openmpi_host_injection.sh         | 26 +------------------
 1 file changed, 1 insertion(+), 25 deletions(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 6b48b0ac04..861a5f4abc 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -43,16 +43,6 @@ parse_cmdline() {
                     exit 1
                 fi
                 ;;
-            --pmix-path)
-                if [ -n "$2"]; then
-                    readonly PMIX_PATH="$2"
-                    shift 2
-                else
-                    echo_red "Error: Argument required for $1"
-                    show_help
-                    exit 1
-                fi
-                ;;
             -t|--temp-dir)
                 if [ -n "$2" ]; then
                     readonly TEMP_DIR="$2"
@@ -171,11 +161,6 @@ inject_mpi() {
             find ${libdir} -maxdepth 1 -type f -name "libpmix.so*" -exec cp {} ${temp_inject_path} \;
             find ${libdir} -maxdepth 1 -type l -name "libpmix.so*" -exec cp -P {} ${host_injection_mpi_path} \;
 
-            local depname deppath
-            while read -r depname deppath; do
-                libs_dict[${depname}]=${deppath}
-            done < <(find ${pmixpath} -maxdepth 1 -name "*.so*" -exec ${system_ldd} {} \; | awk '/=>/ {print $1, $3}' | sort | uniq)
-
             libpath=${host_injection_mpi_path}/$(basename ${libpath})
         fi
 
@@ -219,16 +204,7 @@ inject_mpi() {
                     ${PATCHELF_BIN} --add-needed ${libs_dict[${dep}]} ${lib}
                 fi
             done < <(for dlopen in ${dlopen_libs[@]}; do ${eessi_ldd} ${dlopen}; done \
-                     | grep -e "=> not found" -e "=> ${MPI_PATH}" | awk '!/libmpi\.so.*/ {print $1}' | sort | uniq)
-        fi
-
-        # Inject into libpmix.so non resolved dependencies from dlopen libraries in the PMIX path
-        if [[ ${lib} =~ libpmix\.so ]]; then            
-            while read -r dep; do
-                if ! ${PATCHELF_BIN} --print-needed ${lib} | grep -q "${dep}"; then
-                    ${PATCHELF_BIN} --add-needed ${libs_dict[${dep}]} ${lib}
-                fi
-            done < <(find ${pmixpath} -maxdepth 1 -type f -name "*.so*" -exec ${eessi_ldd} {} \; | awk '/not found/ && !/libpmix\.so.*/ {print $1}' | sort | uniq)
+                     | awk '/not found/ && !/libmpi\.so.*/ {print $1}' | sort | uniq)
         fi
 
     done < <(find ${temp_inject_path} -type f)

From f60394d0f7f1a5fb70fb991419033993c86758c9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Tue, 4 Mar 2025 14:16:34 +0100
Subject: [PATCH 18/20] remove pmix path from parse_cmdline

---
 scripts/mpi_support/install_openmpi_host_injection.sh | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 861a5f4abc..aab42f684c 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -70,11 +70,6 @@ parse_cmdline() {
         exit 0
     fi
 
-    if [ -z "${PMIX_PATH}" ]; then
-        echo_yellow "PMIX path was not specified"
-        echo_yellow "Assuming it is the directory where libpmix is found"
-    fi
-
     readonly CLEAN=${CLEAN:=true}
 }
 

From 6b3c1fd139ca74099d099dd30bff639b4c8795b2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Tue, 4 Mar 2025 15:04:05 +0100
Subject: [PATCH 19/20] improve sanity check

---
 .../install_openmpi_host_injection.sh         | 21 +++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index aab42f684c..1f832f98a4 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -22,7 +22,7 @@ show_help() {
     echo "  --mpi-path /path/to/mpi          Specify the path to the MPI host installation (Required)"
     echo "  -t, --temp-dir /path/to/tmpdir   Specify a location to use for temporary"
     echo "                                   storage during the mpi injection"
-    echo "  --noclean                        Do not remove the temporary directory after finishing injection"
+    echo "  --noclean                        Do not remove the temporary directory and the host injected libraries after finishing injection"
 }
 
 
@@ -205,13 +205,17 @@ inject_mpi() {
     done < <(find ${temp_inject_path} -type f)
 
     # Sanity check MPI injection
+    local sanity=1
     if ${eessi_ldd} ${temp_inject_path}/* &> /dev/null; then
         cp ${temp_inject_path}/* -t ${host_injection_mpi_path}
-        echo_green "MPI injection was successful"
-        return 0
-    else
-        fatal_error "MPI host injection failed. EESSI will use its own MPI libraries"
+        if ${eessi_ldd} ${temp_inject_path}/* | grep -q "not found"; then
+            ${CLEAN} && rm -f ${host_injection_mpi_path}/*.so*
+        else
+            sanity=0
+        fi
     fi
+    
+    return ${sanity}
 }
 
 
@@ -236,7 +240,12 @@ main() {
     echo "Temporary directory for injection: ${tmpdir}"
 
     download_patchelf ${tmpdir}
-    inject_mpi ${tmpdir}
+    
+    if inject_mpi ${tmpdir}; then
+        echo_green "MPI injection was successful"
+    else
+        fatal_error "MPI host injection failed"
+    fi
 
     if ${CLEAN}; then
         rm -rf "${tmpdir}"

From 4dac5da6767edeca2f1cb1cd90774597d5342f34 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pedro=20Fern=C3=A1ndez?= <pedro.fernandez@hpcnow.com>
Date: Tue, 4 Mar 2025 16:32:51 +0100
Subject: [PATCH 20/20] add force cmd option to do MPI injection even if
 already done

---
 .../mpi_support/install_openmpi_host_injection.sh    | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/scripts/mpi_support/install_openmpi_host_injection.sh b/scripts/mpi_support/install_openmpi_host_injection.sh
index 1f832f98a4..3a9872cea7 100755
--- a/scripts/mpi_support/install_openmpi_host_injection.sh
+++ b/scripts/mpi_support/install_openmpi_host_injection.sh
@@ -23,6 +23,7 @@ show_help() {
     echo "  -t, --temp-dir /path/to/tmpdir   Specify a location to use for temporary"
     echo "                                   storage during the mpi injection"
     echo "  --noclean                        Do not remove the temporary directory and the host injected libraries after finishing injection"
+    echo "  --force                          Force MPI injection even if it is already done"
 }
 
 
@@ -57,6 +58,10 @@ parse_cmdline() {
                 CLEAN=false
                 shift 1
                 ;;
+            --force)
+                FORCE=true
+                shift 1
+                ;;
             *)
                 echo_red "Error: Unknown option: $1"
                 show_help
@@ -71,6 +76,7 @@ parse_cmdline() {
     fi
 
     readonly CLEAN=${CLEAN:=true}
+    readonly FORCE=${FORCE:=false}
 }
 
 
@@ -111,7 +117,11 @@ inject_mpi() {
     if [ -d ${host_injection_mpi_path} ]; then
         if [ -n "$(ls -A ${host_injection_mpi_path})" ]; then
             echo "MPI was already injected"
-            return 0
+            if ${FORCE}; then
+                echo "Forcing new MPI injection"
+            else
+                return 0
+            fi
         fi
     fi