Control: tags -1 + patch
On 2017-02-14 14:37, Gilles Filippini wrote:
Source: med-fichier
Version: 3.0.6-11
Severity: grave
Justification: renders package unusable
Hi,
From the Salome Platform support forum [1]:
Problems with Salome and Code Saturne in Debian
Posted by Elektrix at January 03. 2017
Hello all,
I'm trying to set up a CFD case with Salome, export the mesh in a MED
file and then process it with Code Saturne. CS doesn't read the MED
file and gives the error in the preprocessing stage:
_MEDdatasetRd.c [139] : Erreur à la lecture du dataset
_MEDdatasetRd.c [139] : COO
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
#000: ../../../src/H5Dio.c line 170 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ../../../src/H5Dio.c line 418 in H5D__read(): unable to set up
type info
major: Dataset
minor: Unable to initialize object
#002: ../../../src/H5Dio.c line 953 in H5D__typeinfo_init(): not a
datatype
major: Invalid arguments to routine
minor: Inappropriate type
_MEDdatasetRd.c [142] : _dataset = 2
_MEDdatasetRd.c [143] : _i = 0
_MEDdatasetRd.c [144] : (*filter).memspace[_i] = 2
_MEDdatasetRd.c [145] : (*filter).diskspace[_i] = 3
_MEDmeshAdvancedRd30.c [462] : Erreur à la lecture du dataset
_MEDmeshAdvancedRd30.c [462] :
_MEDmeshAdvancedRd30.c [463] : meshname = "Mesh_water"
_MEDmeshAdvancedRd30.c [463] : numit = -1
_MEDmeshAdvancedRd30.c [463] : numdt = -1
_MEDmeshAdvancedRd30.c [463] : _datagroupname2 = "NOE"
_MEDmeshAdvancedRd30.c [464] : _datagroupname3 = ""
_MEDmeshAdvancedRd30.c [464] : _profilename =
"MED_NO_PROFILE_INTERNAL"
The problem can be because I installed Salome from the
SALOME-7.6.0-DB07.tgz archive whilst Code Saturne is a Debian package
and is installed via the Debian package system which is much easier
than installing the original package. So the med and hdf5 libraries of
CS come from the Debian repositories. I can't use newer versions of
Salome (7.7.1 or 7.8.0) as they produce MED3.1 files but my CS reads
only MED3.0 files.
The details of my machine:
Debian stretch (testing) on AMD64
Salome 7.6.0 from SALOME-7.6.0-DB07.tgz
Code Saturne 4.3 Debian package
libmed 3.0.6-10.1 Debian package
hdf5 1.10.0 Debian package
Not knowing if this problem comes from how I create the mesh I tried
to run one of the test cases from the Code Saturne tutorials but ran
into other problems.
If you need any other information pleas let me know. Any hint on how
to go further is very welcome.
Best regards
Elektrix
....
Re: Problems with Salome and Code Saturne in Debian
Posted by Yvan Fournier at Monday 16:21
Hello,
I was contacted by the Debian maintainer relative to this, so it seems
the bug was reported.
The root problem is that the MED library is not compatible with HDF5
1.10 yet. So reverting to HDF5 1.8 as indicated is the solution for
now, but the better solution would be for MED to handle compatibility
with both HDF5 1.8 and HDF5 1.10 (or at least 1.10 for future
versions).
Best regards,
Yvan
[1] http://www.salome-platform.org/forum/forum_9/122041955
Patch proposal attached.
Thanks,
_g
diff -Nru med-fichier-3.0.6/debian/changelog med-fichier-3.0.6/debian/changelog
--- med-fichier-3.0.6/debian/changelog 2016-10-30 18:06:27.000000000 +0100
+++ med-fichier-3.0.6/debian/changelog 2017-02-13 18:02:35.000000000 +0100
@@ -1,3 +1,11 @@
+med-fichier (3.0.6-10.2) unstable; urgency=medium
+
+ * Non-maintainer upload
+ * New patch type_hdf_should_be_hid_t.patch fixing HDF5 1.10 support
+ for the C API (closes: #855130)
+
+ -- Gilles Filippini <p...@debian.org> Mon, 13 Feb 2017 18:02:35 +0100
+
med-fichier (3.0.6-10.1) unstable; urgency=medium
* Non-maintainer upload
diff -Nru med-fichier-3.0.6/debian/patches/series med-fichier-3.0.6/debian/patches/series
--- med-fichier-3.0.6/debian/patches/series 2016-10-20 21:58:54.000000000 +0200
+++ med-fichier-3.0.6/debian/patches/series 2017-02-13 18:02:35.000000000 +0100
@@ -2,3 +2,4 @@
hdf5_link.patch
clang-ftbfs.diff
fix-fid-type-in-medequivinfo.patch
+type_hdf_should_be_hid_t.patch
diff -Nru med-fichier-3.0.6/debian/patches/type_hdf_should_be_hid_t.patch med-fichier-3.0.6/debian/patches/type_hdf_should_be_hid_t.patch
--- med-fichier-3.0.6/debian/patches/type_hdf_should_be_hid_t.patch 1970-01-01 01:00:00.000000000 +0100
+++ med-fichier-3.0.6/debian/patches/type_hdf_should_be_hid_t.patch 2017-02-13 18:02:35.000000000 +0100
@@ -0,0 +1,152 @@
+Index: med-fichier-3.0.6/src/2.3.6/hdfi/MEDdatasetNumLire232.c
+===================================================================
+--- med-fichier-3.0.6.orig/src/2.3.6/hdfi/MEDdatasetNumLire232.c
++++ med-fichier-3.0.6/src/2.3.6/hdfi/MEDdatasetNumLire232.c
+@@ -71,8 +70,8 @@ void _MEDdatasetNumLire232(int dummy,..
+ med_size start_mem[1],start_data[1],*pflmem=0,*pfldsk=0;
+ med_size stride[1],count[1],pcount[1],size[1],pflsize[1];
+ med_err ret;
+- int i,j,index,type_hdf;
+- hid_t datatype;
++ int i,j,index;
++ hid_t datatype,type_hdf;
+ size_t typesize;
+ int dim, firstdim, dimutil, lastdim;
+ med_size sizencmp[1];
+Index: med-fichier-3.0.6/src/2.3.6/hdfi/MEDdatasetNumEcrire231.c
+===================================================================
+--- med-fichier-3.0.6.orig/src/2.3.6/hdfi/MEDdatasetNumEcrire231.c
++++ med-fichier-3.0.6/src/2.3.6/hdfi/MEDdatasetNumEcrire231.c
+@@ -62,8 +62,9 @@ void _MEDdatasetNumEcrire231(int dummy,
+ med_size start_mem[1],start_data[1],*pflmem,*pfldsk;
+ med_size stride[1],count[1],pcount[1],pflsize[1];
+ med_err ret;
+- int i,j,index,type_hdf;
++ int i,j,index;
+ int dim, firstdim, dimutil, lastdim ;
++ hid_t type_hdf;
+ med_mode_acces MED_MODE_ACCES;
+
+ va_start(params,dummy);
+Index: med-fichier-3.0.6/src/2.3.6/hdfi/MEDdatasetNumEcrire232.c
+===================================================================
+--- med-fichier-3.0.6.orig/src/2.3.6/hdfi/MEDdatasetNumEcrire232.c
++++ med-fichier-3.0.6/src/2.3.6/hdfi/MEDdatasetNumEcrire232.c
+@@ -72,9 +72,10 @@ void _MEDdatasetNumEcrire232(int dummy,
+ med_size stride[1],count[1],pcount[1],pflsize[1];
+ med_size datasetsize[1], countncmp=0;
+ med_err ret=-1;
+- int i=0,j=0,index=0,type_hdf=0;
++ int i=0,j=0,index=0;
+ int dim=0, firstdim=0, dimutil=0, lastdim=0 ;
+ int datasetsizeEqualTosizespace = 0;
++ hid_t type_hdf=0;
+ med_mode_acces MED_MODE_ACCES;
+
+ va_start(params,dummy);
+Index: med-fichier-3.0.6/src/2.3.6/hdfi/MEDdatasetNumLire231.c
+===================================================================
+--- med-fichier-3.0.6.orig/src/2.3.6/hdfi/MEDdatasetNumLire231.c
++++ med-fichier-3.0.6/src/2.3.6/hdfi/MEDdatasetNumLire231.c
+@@ -60,8 +60,8 @@ void _MEDdatasetNumLire231(int dummy,..
+ med_size start_mem[1],start_data[1],*pflmem=0,*pfldsk=0;
+ med_size stride[1],count[1],pcount[1],size[1],pflsize[1];
+ med_err ret;
+- int i,j,index,type_hdf;
+- hid_t datatype;
++ int i,j,index;
++ hid_t datatype,type_hdf;
+ size_t typesize;
+ int dim, firstdim, dimutil, lastdim;
+
+Index: med-fichier-3.0.6/src/2.3.6/hdfi/MEDattrNumEcrire.c
+===================================================================
+--- med-fichier-3.0.6.orig/src/2.3.6/hdfi/MEDattrNumEcrire.c
++++ med-fichier-3.0.6/src/2.3.6/hdfi/MEDattrNumEcrire.c
+@@ -36,7 +36,7 @@ med_err _MEDattrNumEcrire(med_idt pere,m
+ {
+ med_idt aid,attr;
+ med_err ret;
+- int type_hdf;
++ hid_t type_hdf;
+ med_mode_acces MED_MODE_ACCES;
+
+ if ( (MED_MODE_ACCES = _MEDmodeAcces(pere) ) == MED_UNDEF_MODE_ACCES ) {
+Index: med-fichier-3.0.6/src/hdfi/_MEDattributeNumRdByName.c
+===================================================================
+--- med-fichier-3.0.6.orig/src/hdfi/_MEDattributeNumRdByName.c
++++ med-fichier-3.0.6/src/hdfi/_MEDattributeNumRdByName.c
+@@ -27,7 +27,7 @@ med_err _MEDattributeNumRdByName(med_idt
+ {
+ med_idt _attid=0;
+ med_err _ret=-1;
+- int type_hdf;
++ hid_t type_hdf;
+
+ switch(type)
+ {
+Index: med-fichier-3.0.6/src/hdfi/_MEDattributeNumWr.c
+===================================================================
+--- med-fichier-3.0.6.orig/src/hdfi/_MEDattributeNumWr.c
++++ med-fichier-3.0.6/src/hdfi/_MEDattributeNumWr.c
+@@ -32,7 +32,7 @@ med_err _MEDattributeNumWr(med_idt pid,
+ {
+ med_idt _attid=0,aid=0;
+ med_err _ret=-1;
+- int type_hdf;
++ hid_t type_hdf;
+ med_access_mode MED_ACCESS_MODE;
+ H5O_info_t _oinfo;
+
+Index: med-fichier-3.0.6/src/hdfi/_MEDattributeNumWrByName.c
+===================================================================
+--- med-fichier-3.0.6.orig/src/hdfi/_MEDattributeNumWrByName.c
++++ med-fichier-3.0.6/src/hdfi/_MEDattributeNumWrByName.c
+@@ -32,7 +32,7 @@ med_err _MEDattributeNumWrByName(med_idt
+ {
+ med_idt _attid=0,aid=0;
+ med_err _ret=-1;
+- int type_hdf;
++ hid_t type_hdf;
+ med_access_mode MED_ACCESS_MODE;
+ H5O_info_t _oinfo;
+
+Index: med-fichier-3.0.6/src/hdfi/_MEDattributeStringRdByName.c
+===================================================================
+--- med-fichier-3.0.6.orig/src/hdfi/_MEDattributeStringRdByName.c
++++ med-fichier-3.0.6/src/hdfi/_MEDattributeStringRdByName.c
+@@ -29,7 +29,7 @@ med_err _MEDattributeStringRdByName(med_
+ {
+ med_err _ret=-1;
+ med_idt _attid=0;
+- int type_hdf=0;
++ hid_t type_hdf=0;
+
+ if ( (type_hdf = H5Tcopy(H5T_C_S1)) < 0) {
+ MED_ERR_(_ret,MED_ERR_CREATE,MED_ERR_HDFTYPE, MED_ERR_NAME_MSG );
+Index: med-fichier-3.0.6/src/hdfi/_MEDattributeStringWr.c
+===================================================================
+--- med-fichier-3.0.6.orig/src/hdfi/_MEDattributeStringWr.c
++++ med-fichier-3.0.6/src/hdfi/_MEDattributeStringWr.c
+@@ -30,7 +30,7 @@ med_err _MEDattributeStringWr(med_idt pi
+ med_access_mode MED_ACCESS_MODE;
+ med_idt _attid=0,aid=0;
+ med_err _ret=-1;
+- int type_hdf=0;
++ hid_t type_hdf=0;
+ med_bool _attmustbecreated= MED_FALSE;
+ hsize_t _attsize=0;
+ med_size _valsize=0;
+Index: med-fichier-3.0.6/src/hdfi/_MEDattributeStringWrByName.c
+===================================================================
+--- med-fichier-3.0.6.orig/src/hdfi/_MEDattributeStringWrByName.c
++++ med-fichier-3.0.6/src/hdfi/_MEDattributeStringWrByName.c
+@@ -31,7 +31,7 @@ med_err _MEDattributeStringWrByName(med_
+ med_access_mode MED_ACCESS_MODE;
+ med_idt _attid=0,aid=0;
+ med_err _ret=-1;
+- int type_hdf=0;
++ hid_t type_hdf=0;
+ med_bool _attmustbecreated= MED_FALSE;
+ hsize_t _attsize=0;
+ med_size _valsize=0;
--
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
