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CDO package: Fix build with gcc@9 (#11464)

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This makes several changes to make CDO work with gcc@9:

- Add version 1.9.7rc2
- Add a patch to make version 1.9.7rc2 build with gcc@9:
- Add a conflict with GCC 9 for earlier versions of CDO

It also adds a pkgconfig build dependency as configure checks for it.
This commit is contained in:
Michael Kuhn 2019-05-17 02:53:38 +02:00 committed by Peter Scheibel
parent 8675f44d45
commit e90b4ce6fb
2 changed files with 212 additions and 0 deletions
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202
var/spack/repos/builtin/packages/cdo/gcc9-openmp-1.9.7rc2.patch Normal file
View file

@ -0,0 +1,202 @@
Only in cdo-1.9.7rc2: .spack_patched
diff -ru cdo-1.9.7rc2.orig/src/after_sptrans.cc cdo-1.9.7rc2/src/after_sptrans.cc
--- cdo-1.9.7rc2.orig/src/after_sptrans.cc 2019-04-23 08:10:06.000000000 +0200
+++ cdo-1.9.7rc2/src/after_sptrans.cc 2019-05-15 08:24:25.815215686 +0200
@@ -300,7 +300,7 @@
#endif
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(nlat, poli, pold, pdev, pol2, pol3, coslat, gmu, gwt, PlanetRadius)
+#pragma omp parallel for default(none) shared(nlat, poli, pold, pdev, pol2, pol3, coslat, gmu, gwt, PlanetRadius) firstprivate(dimsp, waves)
#endif
for (long jgl = 0; jgl < nlat; ++jgl)
{
@@ -357,7 +357,7 @@
for (long jgl = 0; jgl < nlat; ++jgl) coslat[jgl] = sqrt(1.0 - gmu[jgl] * gmu[jgl]);
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(nlat, ntr, pnm2, work2, gwt, gmu, poli, pold)
+#pragma omp parallel for default(none) shared(nlat, ntr, pnm2, work2, gwt, gmu, poli, pold) firstprivate(waves)
#endif
for (long jgl = 0; jgl < nlat / 2; jgl++)
{
diff -ru cdo-1.9.7rc2.orig/src/Detrend.cc cdo-1.9.7rc2/src/Detrend.cc
--- cdo-1.9.7rc2.orig/src/Detrend.cc 2019-04-25 08:15:01.000000000 +0200
+++ cdo-1.9.7rc2/src/Detrend.cc 2019-05-15 08:23:37.141221282 +0200
@@ -116,7 +116,7 @@
for (levelID = 0; levelID < nlevels; levelID++)
{
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(array1, array2, vars, varID, levelID)
+#pragma omp parallel for default(none) shared(array1, array2, vars, varID, levelID) firstprivate(gridsize, nsteps, missval)
#endif
for (size_t i = 0; i < gridsize; i++)
{
diff -ru cdo-1.9.7rc2.orig/src/Ensstat3.cc cdo-1.9.7rc2/src/Ensstat3.cc
--- cdo-1.9.7rc2.orig/src/Ensstat3.cc 2019-04-29 08:29:05.000000000 +0200
+++ cdo-1.9.7rc2/src/Ensstat3.cc 2019-05-15 08:23:37.141221282 +0200
@@ -289,7 +289,7 @@
for (int recID = 0; recID < nrecs0; recID++)
{
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(ef) private(streamID, nmiss) lastprivate(varID, levelID)
+#pragma omp parallel for default(none) shared(ef) private(streamID, nmiss) lastprivate(varID, levelID) firstprivate(nfiles)
#endif
for (int fileID = 0; fileID < nfiles; fileID++)
{
diff -ru cdo-1.9.7rc2.orig/src/field2.cc cdo-1.9.7rc2/src/field2.cc
--- cdo-1.9.7rc2.orig/src/field2.cc 2019-04-23 08:52:14.000000000 +0200
+++ cdo-1.9.7rc2/src/field2.cc 2019-05-15 08:23:37.141221282 +0200
@@ -178,7 +178,7 @@
else
{
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(array1, array2, w)
+#pragma omp parallel for default(none) shared(array1, array2, w) firstprivate(len)
#endif
for (size_t i = 0; i < len; i++) array1[i] += w * array2[i];
}
@@ -188,7 +188,7 @@
* Compute the occurrence of values in field, if they do not equal refval.
* This can be used to compute the lengths of multiple periods in a timeseries.
* Missing field values are handled like refval, i.e. they stop a running period.
- * If there is missing data in the occurence field, missing fields values do not
+ * If there is missing data in the occurence field, missing fields values do not
* change anything (they do not start a non-period by setting occurrence to zero).
*/
void
diff -ru cdo-1.9.7rc2.orig/src/Fillmiss.cc cdo-1.9.7rc2/src/Fillmiss.cc
--- cdo-1.9.7rc2.orig/src/Fillmiss.cc 2019-04-23 09:36:07.000000000 +0200
+++ cdo-1.9.7rc2/src/Fillmiss.cc 2019-05-15 08:23:37.141221282 +0200
@@ -469,7 +469,7 @@
#ifdef _OPENMP
#pragma omp parallel for default(none) \
- shared(knnWeights, findex, mindex, vindex, array1, array2, xvals, yvals, gps, numNeighbors)
+ shared(knnWeights, findex, mindex, vindex, array1, array2, xvals, yvals, gps, numNeighbors) firstprivate(nmiss)
#endif
for (size_t i = 0; i < nmiss; ++i)
{
diff -ru cdo-1.9.7rc2.orig/src/grid_area.cc cdo-1.9.7rc2/src/grid_area.cc
--- cdo-1.9.7rc2.orig/src/grid_area.cc 2019-05-09 14:03:25.000000000 +0200
+++ cdo-1.9.7rc2/src/grid_area.cc 2019-05-15 08:23:37.141221282 +0200
@@ -365,7 +365,7 @@
Progress::init();
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(nlon, findex, area, nv, grid_corner_lon, grid_corner_lat)
+#pragma omp parallel for default(none) shared(nlon, findex, area, nv, grid_corner_lon, grid_corner_lat) firstprivate(gridsize)
#endif
for (size_t i = 0; i < gridsize; ++i)
{
@@ -501,7 +501,7 @@
#ifdef _OPENMP
#pragma omp parallel for default(none) \
- shared(findex, area, grid_corner_lon, grid_corner_lat, grid_center_lon, grid_center_lat)
+ shared(findex, area, grid_corner_lon, grid_corner_lat, grid_center_lon, grid_center_lat) firstprivate(gridsize, nv)
#endif
for (size_t i = 0; i < gridsize; ++i)
{
diff -ru cdo-1.9.7rc2.orig/src/Intlevel.cc cdo-1.9.7rc2/src/Intlevel.cc
--- cdo-1.9.7rc2.orig/src/Intlevel.cc 2019-03-07 08:32:03.000000000 +0100
+++ cdo-1.9.7rc2/src/Intlevel.cc 2019-05-15 08:23:37.141221282 +0200
@@ -74,7 +74,7 @@
const double *var1L2 = vardata1 + gridsize * idx2;
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(gridsize, var2, var1L1, var1L2, missval)
+#pragma omp parallel for default(none) shared(gridsize, var2, var1L1, var1L2, missval) firstprivate(wgt1, wgt2)
#endif
for (size_t i = 0; i < gridsize; ++i)
{
@@ -96,7 +96,7 @@
double *var2 = vardata2 + offset;
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(gridsize, vardata1, var2, lev_idx1, lev_idx2, lev_wgt1, lev_wgt2, missval)
+#pragma omp parallel for default(none) shared(gridsize, vardata1, var2, lev_idx1, lev_idx2, lev_wgt1, lev_wgt2, missval) firstprivate(offset)
#endif
for (size_t i = 0; i < gridsize; i++)
{
diff -ru cdo-1.9.7rc2.orig/src/Runstat.cc cdo-1.9.7rc2/src/Runstat.cc
--- cdo-1.9.7rc2.orig/src/Runstat.cc 2019-04-04 08:17:54.000000000 +0200
+++ cdo-1.9.7rc2/src/Runstat.cc 2019-05-15 08:23:37.141221282 +0200
@@ -164,7 +164,7 @@
for (size_t i = 0; i < fieldsize; i++) samp1[tsID][varID][levelID].vec[i] = (double) imask[i];
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(tsID, imask, samp1, varID, levelID)
+#pragma omp parallel for default(none) shared(tsID, imask, samp1, varID, levelID) firstprivate(fieldsize)
#endif
for (int inp = 0; inp < tsID; inp++)
{
@@ -200,7 +200,7 @@
else
{
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(tsID, vars1, varID, levelID, rvars1)
+#pragma omp parallel for default(none) shared(tsID, vars1, varID, levelID, rvars1) firstprivate(operfunc)
#endif
for (int inp = 0; inp < tsID; inp++)
{
@@ -314,7 +314,7 @@
for (size_t i = 0; i < fieldsize; i++) samp1[ndates - 1][varID][levelID].vec[i] = (double) imask[i];
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(imask, samp1, varID, levelID)
+#pragma omp parallel for default(none) shared(imask, samp1, varID, levelID) firstprivate(ndates, fieldsize)
#endif
for (int inp = 0; inp < ndates - 1; inp++)
{
@@ -328,7 +328,7 @@
{
vfarmoq(vars2[ndates - 1][varID][levelID], vars1[ndates - 1][varID][levelID]);
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(vars1, vars2, varID, levelID, rvars1)
+#pragma omp parallel for default(none) shared(vars1, vars2, varID, levelID, rvars1) firstprivate(ndates)
#endif
for (int inp = 0; inp < ndates - 1; inp++)
{
@@ -339,7 +339,7 @@
else if (lrange)
{
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(vars1, vars2, varID, levelID, rvars1)
+#pragma omp parallel for default(none) shared(vars1, vars2, varID, levelID, rvars1) firstprivate(ndates)
#endif
for (int inp = 0; inp < ndates - 1; inp++)
{
@@ -350,7 +350,7 @@
else
{
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(vars1, varID, levelID, rvars1)
+#pragma omp parallel for default(none) shared(vars1, varID, levelID, rvars1) firstprivate(ndates, operfunc)
#endif
for (int inp = 0; inp < ndates - 1; inp++)
{
diff -ru cdo-1.9.7rc2.orig/src/Timsort.cc cdo-1.9.7rc2/src/Timsort.cc
--- cdo-1.9.7rc2.orig/src/Timsort.cc 2019-03-18 08:17:00.000000000 +0100
+++ cdo-1.9.7rc2/src/Timsort.cc 2019-05-15 08:23:37.141221282 +0200
@@ -109,7 +109,7 @@
for (levelID = 0; levelID < nlevels; levelID++)
{
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(sarray, vars, varID, levelID)
+#pragma omp parallel for default(none) shared(sarray, vars, varID, levelID) firstprivate(gridsize, nts)
#endif
for (size_t i = 0; i < gridsize; i++)
{
diff -ru cdo-1.9.7rc2.orig/src/Tstepcount.cc cdo-1.9.7rc2/src/Tstepcount.cc
--- cdo-1.9.7rc2.orig/src/Tstepcount.cc 2019-04-23 09:44:13.000000000 +0200
+++ cdo-1.9.7rc2/src/Tstepcount.cc 2019-05-15 08:23:37.141221282 +0200
@@ -120,7 +120,7 @@
for (levelID = 0; levelID < nlevels; levelID++)
{
#ifdef _OPENMP
-#pragma omp parallel for default(none) shared(mem, vars, varID, levelID) schedule(dynamic, 1)
+#pragma omp parallel for default(none) shared(mem, vars, varID, levelID) schedule(dynamic, 1) firstprivate(gridsize, nts, refval, missval)
#endif
for (size_t i = 0; i < gridsize; i++)
{

10
var/spack/repos/builtin/packages/cdo/package.py
View file

@ -17,6 +17,7 @@ class Cdo(AutotoolsPackage):
maintainers = ['skosukhin']
version('1.9.7rc2', '62313bdf60860693e96494fd2fd8ff48e65266f600f6ae8c817e46a652e6b215', url='https://code.mpimet.mpg.de/attachments/download/19883/cdo-1.9.7rc2.tar.gz')
version('1.9.6', '322f56c5e13f525c585ee5318d4435db', url='https://code.mpimet.mpg.de/attachments/download/19299/cdo-1.9.6.tar.gz')
version('1.9.5', '0c60f2c94dc5c76421ecf363153a5043', url='https://code.mpimet.mpg.de/attachments/download/18264/cdo-1.9.5.tar.gz')
version('1.9.4', '377c9e5aa7d8cbcb4a6c558abb2eb053', url='https://code.mpimet.mpg.de/attachments/download/17374/cdo-1.9.4.tar.gz')
@ -27,6 +28,11 @@ class Cdo(AutotoolsPackage):
version('1.8.2', '6a2e2f99b7c67ee9a512c40a8d4a7121', url='https://code.mpimet.mpg.de/attachments/download/14686/cdo-1.8.2.tar.gz')
version('1.7.2', 'f08e4ce8739a4f2b63fc81a24db3ee31', url='https://code.mpimet.mpg.de/attachments/download/12760/cdo-1.7.2.tar.gz')
# The build fails due to changes to OpenMP data sharing in GCC 9.
# See: https://gcc.gnu.org/gcc-9/porting_to.html#ompdatasharing
# See: https://code.mpimet.mpg.de/issues/9038 (not public)
patch('gcc9-openmp-1.9.7rc2.patch', when='@1.9.7rc2%gcc@9:')
variant('netcdf', default=True, description='Enable NetCDF support')
variant('grib2', default='eccodes', values=('eccodes', 'grib-api', 'none'),
description='Specify GRIB2 backend')
@ -47,6 +53,8 @@ class Cdo(AutotoolsPackage):
description='Enable Magics library support')
variant('openmp', default=True, description='Enable OpenMP support')
depends_on('pkgconfig', type='build')
depends_on('netcdf', when='+netcdf')
# In this case CDO does not depend on hdf5 directly but we need the backend
# of netcdf to be thread safe.
@ -71,6 +79,8 @@ class Cdo(AutotoolsPackage):
msg='Eccodes is supported starting version 1.9.0')
conflicts('+szip', when='+external-grib1 grib2=none',
msg='The configuration does not support GRIB1')
conflicts('%gcc@9:', when='@:1.9.6',
msg='GCC 9 changed OpenMP data sharing behavior')
def configure_args(self):
config_args = self.with_or_without('netcdf', activation_value='prefix')