apply patch to openmpi to allow running as root inside Docker

.gitlab-ci.yml

@@ -11,6 +11,7 @@ include:
     - apt-get install --yes --no-install-recommends ssh
     - curl https://download.open-mpi.org/release/open-mpi/v${OPENMPI_VER}/openmpi-${OPENMPI_VER_FULL}.tar.gz --output openmpi.tar.gz
     - tar xf openmpi.tar.gz
+    - patch -p1 -d openmpi-${OPENMPI_VER_FULL} < conf/ompi_rootenv.patch
     - pushd openmpi-${OPENMPI_VER_FULL}
     - ./configure --with-cuda --prefix=${HOME}/mpi
     - make -j

conf/ompi_rootenv.patch

@@ -0,0 +1,28 @@
+Allow override environment variables to work. This is required for running as root inside a docker container (e.g. Gitlab CI)
+
+See https://github.com/open-mpi/ompi/pull/5597#issuecomment-520612783
+--- a/orte/tools/orterun/orterun.c
++++ b/orte/tools/orterun/orterun.c
+@@ -143,6 +143,14 @@ int orterun(int argc, char *argv[])
+      * exit with a giant warning flag
+      */
+     if (0 == geteuid() && !orte_cmd_options.run_as_root) {
++        char *r1, *r2;
++        if (NULL != (r1 = getenv("OMPI_ALLOW_RUN_AS_ROOT")) &&
++            NULL != (r2 = getenv("OMPI_ALLOW_RUN_AS_ROOT_CONFIRM"))) {
++            if (0 == strcmp(r1, "1") && 0 == strcmp(r2, "1")) {
++                goto moveon;
++            }
++        }
++
+         fprintf(stderr, "--------------------------------------------------------------------------\n");
+         if (NULL != orte_cmd_options.help) {
+             fprintf(stderr, "%s cannot provide the help message when run as root.\n", orte_basename);
+@@ -160,6 +168,7 @@ int orterun(int argc, char *argv[])
+         exit(1);
+     }
+
++  moveon:
+     /* setup to listen for commands sent specifically to me, even though I would probably
+      * be the one sending them! Unfortunately, since I am a participating daemon,
+      * there are times I need to send a command to "all daemons", and that means *I* have