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science/silo: update 4.11-68 → 4.12.0

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Reported by:	portscout
This commit is contained in:
Yuri Victorovich
2025-11-23 11:10:23 -08:00
parent df2e8bccc8
commit f04154321a
16 changed files with 35 additions and 115 deletions
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misc/lbann/Makefile
+1 -1
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@@ -2,7 +2,7 @@ PORTNAME= lbann
DISTVERSIONPREFIX= v
DISTVERSION= 0.102-254
DISTVERSIONSUFFIX= -g2e3012a9a
PORTREVISION= 4
PORTREVISION= 5
CATEGORIES= misc # machine-learning
MAINTAINER= yuri@FreeBSD.org
science/ascent/Makefile
+1
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@@ -1,6 +1,7 @@
PORTNAME= ascent
DISTVERSIONPREFIX= v
DISTVERSION= 0.9.5
PORTREVISION= 1
CATEGORIES= science
PKGNAMESUFFIX= -visualizer
science/axom/Makefile
+1 -1
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@@ -1,7 +1,7 @@
PORTNAME= axom
DISTVERSIONPREFIX= v
DISTVERSION= 0.10.1
PORTREVISION= 2
PORTREVISION= 3
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
science/conduit/Makefile
+1
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@@ -1,6 +1,7 @@
PORTNAME= conduit
DISTVERSIONPREFIX= v
DISTVERSION= 0.9.5
PORTREVISION= 1
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
science/parthenon/Makefile
+1 -1
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@@ -1,7 +1,7 @@
PORTNAME= parthenon
DISTVERSIONPREFIX= v
DISTVERSION= 24.08
PORTREVISION= 2
PORTREVISION= 3
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
science/polytope/Makefile
+1
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@@ -1,5 +1,6 @@
PORTNAME= polytope
DISTVERSION= 0.7.4
PORTREVISION= 1
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
science/serac/Makefile
+1 -1
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@@ -1,6 +1,6 @@
PORTNAME= serac
PORTVERSION= g20220823
PORTREVISION= 6
PORTREVISION= 7
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
science/silo/Makefile
+2 -3
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@@ -1,7 +1,5 @@
PORTNAME= silo
DISTVERSION= 4.11-68
PORTREVISION= 1
DISTVERSIONSUFFIX= -g819658e
DISTVERSION= 4.12.0
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
@@ -19,6 +17,7 @@ USE_GITHUB= yes
GH_ACCOUNT= LLNL
GH_PROJECT= Silo
CMAKE_ON= SILO_ENABLE_INSTALL_LITE_HEADERS
CMAKE_TESTING_ON= SILO_ENABLE_TESTS # 3 tests fail, see https://github.com/LLNL/Silo/issues/289
CMAKE_TESTING_TARGET= check
science/silo/distinfo
+3 -3
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@@ -1,3 +1,3 @@
TIMESTAMP = 1670041617
SHA256 (LLNL-Silo-4.11-68-g819658e_GH0.tar.gz) = 3a7a75e196c9e39922998054378efa02b2d24dc57ab126ab15a631e2645bd0ce
SIZE (LLNL-Silo-4.11-68-g819658e_GH0.tar.gz) = 14028123
TIMESTAMP = 1763923185
SHA256 (LLNL-Silo-4.12.0_GH0.tar.gz) = 5251816e43b08c19c925480b2daf85cc9b75e494b91df37df0eacc092279cfd0
SIZE (LLNL-Silo-4.12.0_GH0.tar.gz) = 99198889
science/silo/files/patch-CMakeLists.txt
+13
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@@ -0,0 +1,13 @@
- workaround for https://github.com/LLNL/Silo/issues/501
--- CMakeLists.txt.orig 2025-11-23 19:03:43 UTC
+++ CMakeLists.txt
@@ -700,7 +700,7 @@ install(FILES ${silo_public_headers} DESTINATION ${CMA
WORLD_READ)
# Symlink old style silo_f77.inc
-if(SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER)
+if(FALSE AND SILO_ENABLE_FORTRAN AND CMAKE_Fortran_COMPILER)
install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink silo.inc silo_f77.inc
WORKING_DIRECTORY ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR})")
endif()
science/silo/files/patch-git-commit-be29ddf
-44
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@@ -1,44 +0,0 @@
commit be29ddf0352bc8e5a7eecc8772a3acb64dfde18c
Author: miller86 <miller86@llnl.gov>
Date: Fri Dec 2 19:00:20 2022 -0800
fix obj-case-macro
diff --git src/hdf5_drv/silo_hdf5.c src/hdf5_drv/silo_hdf5.c
index 17af250..c45d689 100644
--- src/hdf5_drv/silo_hdf5.c
+++ src/hdf5_drv/silo_hdf5.c
@@ -1809,7 +1809,7 @@ db_hdf5_cwg(DBfile *_dbfile)
*dscount = m.MEMCNT; \
*dsnames = (char **) calloc(*dscount, sizeof(char**)); \
for (i = 0; i < *dscount; i++) \
- (*dsnames)[i] = strdup(m.MEMNAME[i]); \
+ (*dsnames)[i] = strdup(m.MEMNAME); \
break; \
}
@@ -1857,15 +1857,15 @@ db_hdf5_get_obj_dsnames(DBfile *_dbfile, char const *name, int *dscount, char **
switch(_objtype)
{
- DB_OBJ_CASE(DB_QUADVAR, DBquadvar_mt, nvals, value)
- /*DB_OBJ_CASE(DB_QUAD_RECT, DBquadmesh_mt, nspace, coord) wont work for rect case */
- DB_OBJ_CASE(DB_QUAD_CURV, DBquadmesh_mt, nspace, coord)
- DB_OBJ_CASE(DB_QUADMESH, DBquadmesh_mt, nspace, coord)
- DB_OBJ_CASE(DB_UCDVAR, DBucdvar_mt, nvals, value)
- DB_OBJ_CASE(DB_UCDMESH, DBucdmesh_mt, ndims, coord)
- DB_OBJ_CASE(DB_POINTVAR, DBpointvar_mt, nvals, data)
- DB_OBJ_CASE(DB_POINTMESH, DBpointmesh_mt, ndims, coord)
- DB_OBJ_CASE(DB_CSGVAR, DBcsgvar_mt, nvals, vals)
+ DB_OBJ_CASE(DB_QUADVAR, DBquadvar_mt, nvals, value[i])
+ /*DB_OBJ_CASE(DB_QUAD_RECT, DBquadmesh_mt, nspace, coord[i]) wont work for rect case */
+ DB_OBJ_CASE(DB_QUAD_CURV, DBquadmesh_mt, nspace, coord[i])
+ DB_OBJ_CASE(DB_QUADMESH, DBquadmesh_mt, nspace, coord[i])
+ DB_OBJ_CASE(DB_UCDVAR, DBucdvar_mt, nvals, value[i])
+ DB_OBJ_CASE(DB_UCDMESH, DBucdmesh_mt, ndims, coord[i])
+ DB_OBJ_CASE(DB_POINTVAR, DBpointvar_mt, nvals, data[i])
+ DB_OBJ_CASE(DB_POINTMESH, DBpointmesh_mt, ndims, coord[i])
+ DB_OBJ_CASE(DB_CSGVAR, DBcsgvar_mt, nvals, vals[i])
DB_OBJ_CASE(DB_CURVE, DBcurve_mt, npts?1:1, yvarname)
}
H5Tclose(o);
science/silo/files/patch-src_silo_silo.c
-39
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@@ -1,39 +0,0 @@
--- src/silo/silo.c.orig 2022-12-03 02:30:10 UTC
+++ src/silo/silo.c
@@ -238,12 +238,8 @@ typedef struct db_silo_stat_t {
#ifndef SIZEOF_OFF64_T
#error missing definition for SIZEOF_OFF64_T in silo_private.h
#else
-#if SIZEOF_OFF64_T > 4
- struct stat64 s;
-#else
struct stat s;
#endif
-#endif
#ifdef _WIN32
DWORD fileindexlo;
DWORD fileindexhi;
@@ -2121,11 +2117,7 @@ db_silo_stat_one_file(const char *name, db_silo_stat_t
errno = 0;
memset(&(statbuf->s), 0, sizeof(statbuf->s));
-#if SIZEOF_OFF64_T > 4
- retval = stat64(name, &(statbuf->s));
-#else
retval = stat(name, &(statbuf->s));
-#endif /* #if SIZEOF_OFF64_T > 4 */
#ifdef _WIN32
if (retval == 0)
@@ -4136,11 +4128,7 @@ DBOpenReal(const char *name, int type, int mode)
/********************************/
/* System level error occured. */
/********************************/
-#if SIZEOF_OFF64_T > 4
- printf("stat64() failed with error: ");
-#else
printf("stat() failed with error: ");
-#endif
switch (errno)
{
case EACCES: printf("EACCES\n"); break;
science/silo/files/patch-src_silo_silo__json.c
+2 -2
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@@ -1,6 +1,6 @@
--- src/silo/silo_json.c.orig 2022-12-03 02:30:10 UTC
--- src/silo/silo_json.c.orig 2025-11-21 05:30:59 UTC
+++ src/silo/silo_json.c
@@ -441,11 +441,7 @@ json_object_from_binary_file(char const *filename)
@@ -446,11 +446,7 @@ json_object_from_binary_file(char const *filename)
#ifndef SIZEOF_OFF64_T
#error missing definition for SIZEOF_OFF64_T in silo_private.h
#else
science/silo/files/patch-tests_CMake_SiloMakeCheckRunner.cmake
-13
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@@ -1,13 +0,0 @@
- workaround for https://github.com/LLNL/Silo/issues/288
--- tests/CMake/SiloMakeCheckRunner.cmake.orig 2022-12-03 06:53:38 UTC
+++ tests/CMake/SiloMakeCheckRunner.cmake
@@ -72,7 +72,7 @@ function(silo_add_make_check_runner)
message(WARNING "silo_add_make_check_runner: NAME argument is required.")
return()
endif()
- set(test_cmd ${samcr_NAME})
+ set(test_cmd "./${samcr_NAME}")
if("ARGS" IN_LIST samcr_KEYWORDS_MISSING_VALUES)
message(WARNING "silo_add_make_check_runner: ARGS argument provided without a value.")
return()
science/silo/pkg-plist
+7 -6
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@@ -3,18 +3,19 @@
%%SILOCK%%bin/silock
%%BROWSER%%bin/silodiff
%%BROWSER%%bin/silofile
cmake/SiloConfig.cmake
cmake/SiloConfigVersion.cmake
cmake/SiloTargets-%%CMAKE_BUILD_TYPE%%.cmake
cmake/SiloTargets.cmake
include/lite_pdb.h
include/lite_score.h
include/pdform.h
include/pmpio.h
include/silo.h
include/silo.inc
%%FORTRAN%%include/silo.inc
%%FORTRAN%%include/silo_FC.h
include/silo_exports.h
include/silo_f9x.inc
%%PYTHON%%lib/Silo.so
lib/cmake/Silo/SiloConfig.cmake
lib/cmake/Silo/SiloConfigVersion.cmake
lib/cmake/Silo/SiloTargets-%%CMAKE_BUILD_TYPE%%.cmake
lib/cmake/Silo/SiloTargets.cmake
lib/libsilo%%SUFX_HDF5%%.so
lib/libsilo%%SUFX_HDF5%%.so.4.12.0
lib/libsilo%%SUFX_HDF5%%.so.412
science/spheral/Makefile
+1 -1
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@@ -1,7 +1,7 @@
PORTNAME= spheral
DISTVERSIONPREFIX= v
DISTVERSION= 2025.06.1
PORTREVISION= 3
PORTREVISION= 4
CATEGORIES= science # physics
MAINTAINER= yuri@FreeBSD.org