- Update net/openmpi to 4.0.3 (openmpi 1 is deprecated)

- Remove option for net/openmpi2 from science/pnetcdf (net/openmpi2 is deprecated and will be removed)
- Fix science/gromacs plist when MPI option is enabled
- Bump PORTREVISION for all the consumers of net/openmpi

1 files changed, 20 insertions, 0 deletions

diff --git a/net/openmpi/files/patch-opal_mca_pmix_pmix3x_pmix_src_mca_pshmem_mmap_pshmem__mmap.c b/net/openmpi/files/patch-opal_mca_pmix_pmix3x_pmix_src_mca_pshmem_mmap_pshmem__mmap.c
new file mode 100644
index 000000000000..2718655bf401
--- /dev/null
+++ b/net/openmpi/files/patch-opal_mca_pmix_pmix3x_pmix_src_mca_pshmem_mmap_pshmem__mmap.c
@@ -0,0 +1,20 @@
+--- opal/mca/pmix/pmix3x/pmix/src/mca/pshmem/mmap/pshmem_mmap.c.orig	2020-04-12 11:49:10 UTC
++++ opal/mca/pmix/pmix3x/pmix/src/mca/pshmem/mmap/pshmem_mmap.c
+@@ -79,6 +79,9 @@ static int _mmap_segment_create(pmix_pshmem_seg_t *sm_
+     if (0 != (rc = posix_fallocate(sm_seg->seg_id, 0, size))) {
+         pmix_output_verbose(2, pmix_globals.debug_output,
+                 "sys call posix_fallocate(2) fail\n");
++        if (EINVAL == rc) {
++            goto ftruncate;
++        }
+         if (ENOSPC == rc) {
+             rc = PMIX_ERR_OUT_OF_RESOURCE;
+             goto out;
+@@ -98,6 +101,7 @@ static int _mmap_segment_create(pmix_pshmem_seg_t *sm_
+         goto map_memory;
+     }
+ #endif
++ftruncate:
+     if (0 != ftruncate(sm_seg->seg_id, size)) {
+         pmix_output_verbose(2, pmix_globals.debug_output,
+                 "sys call ftruncate(2) fail\n");