[SOLVED] Problem upgrading STA10.2

todd_alan_martin · 2010-12-15 07:23:03

I successfully installed code-aster 10.2.0 with the acml libraries, but now when I run the upgrade, I get the following error. Can anyone shed some light on this?

Thanks,
Todd.

Build Code_Aster executable

extracting 'python.o' from libasterd.a... [ OK ]
creating .../STA10.2.x/asterd... [FAILED]
Exit code : 256
/usr/bin/ld: skipping incompatible /usr/lib/libieee.a when searching for -lieee
/usr/bin/ld: skipping incompatible /usr/lib/libdl.so when searching for -ldl
/usr/bin/ld: skipping incompatible /usr/lib/libutil.so when searching for -lutil
/usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz
/usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz
/usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/usr/bin/ld: skipping incompatible /usr/lib/libgcc_s.so when searching for -lgcc_s
/usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/usr/bin/ld: skipping incompatible /usr/lib/libgcc_s.so when searching for -lgcc_s
/usr/bin/ld: Dwarf Error: Offset (108) greater than or equal to .debug_str size (51).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfopd.o): In function `hdfopd_':
/opt/aster/STA10.2/bibc/hdf/hdfopd.c:62: undefined reference to `H5Dopen'
/usr/bin/ld: Dwarf Error: Offset (114) greater than or equal to .debug_str size (51).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfopg.o): In function `hdfopg_':
/opt/aster/STA10.2/bibc/hdf/hdfopg.c:55: undefined reference to `H5Gopen'
/usr/bin/ld: Dwarf Error: Offset (90) greater than or equal to .debug_str size (45).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfopf.o): In function `hdfopf_':
/opt/aster/STA10.2/bibc/hdf/hdfopf.c:45: undefined reference to `H5check_version'
/opt/aster/STA10.2/bibc/hdf/hdfopf.c:45: undefined reference to `H5Fopen'
/usr/bin/ld: Dwarf Error: Offset (192) greater than or equal to .debug_str size (82).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfrat.o): In function `hdfrat_':
/opt/aster/STA10.2/bibc/hdf/hdfrat.c:52: undefined reference to `H5Aopen_name'
/opt/aster/STA10.2/bibc/hdf/hdfrat.c:53: undefined reference to `H5Aget_type'
/opt/aster/STA10.2/bibc/hdf/hdfrat.c:54: undefined reference to `H5Tget_size'
/opt/aster/STA10.2/bibc/hdf/hdfrat.c:55: undefined reference to `H5Aget_space'
/opt/aster/STA10.2/bibc/hdf/hdfrat.c:56: undefined reference to `H5Sget_simple_extent_ndims'
/opt/aster/STA10.2/bibc/hdf/hdfrat.c:57: undefined reference to `H5Sget_simple_extent_dims'
/opt/aster/STA10.2/bibc/hdf/hdfrat.c:58: undefined reference to `H5Aread'
/opt/aster/STA10.2/bibc/hdf/hdfrat.c:61: undefined reference to `H5Aclose'
/usr/bin/ld: Dwarf Error: Offset (109) greater than or equal to .debug_str size (75).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfnbo.o): In function `hdfnbo_':
/opt/aster/STA10.2/bibc/hdf/hdfnbo.c:53: undefined reference to `H5Giterate'
/usr/bin/ld: Dwarf Error: Offset (238) greater than or equal to .debug_str size (64).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfnom.o): In function `hdfnom_':
/opt/aster/STA10.2/bibc/hdf/hdfnom.c:52: undefined reference to `H5Giterate'
/opt/aster/STA10.2/bibc/hdf/hdfnom.c:58: undefined reference to `H5Giterate'
/usr/bin/ld: Dwarf Error: Offset (66) greater than or equal to .debug_str size (45).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfclg.o): In function `hdfclg_':
/opt/aster/STA10.2/bibc/hdf/hdfclg.c:34: undefined reference to `H5Gclose'
/usr/bin/ld: Dwarf Error: Offset (86) greater than or equal to .debug_str size (45).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfcrf.o): In function `hdfcrf_':
/opt/aster/STA10.2/bibc/hdf/hdfcrf.c:46: undefined reference to `H5check_version'
/opt/aster/STA10.2/bibc/hdf/hdfcrf.c:46: undefined reference to `H5Fcreate'
/usr/bin/ld: Dwarf Error: Offset (366) greater than or equal to .debug_str size (232).
/opt/aster/STA10.2.x/lib/libasterd.a(hdftsd.o): In function `hdftsd_':
/opt/aster/STA10.2/bibc/hdf/hdftsd.c:42: undefined reference to `H5Dget_type'
/opt/aster/STA10.2/bibc/hdf/hdftsd.c:43: undefined reference to `H5Tget_class'
/opt/aster/STA10.2/bibc/hdf/hdftsd.c:52: undefined reference to `H5Tget_size'
/opt/aster/STA10.2/bibc/hdf/hdftsd.c:53: undefined reference to `H5Dget_space'
/opt/aster/STA10.2/bibc/hdf/hdftsd.c:54: undefined reference to `H5Sget_simple_extent_ndims'
/opt/aster/STA10.2/bibc/hdf/hdftsd.c:55: undefined reference to `H5Sget_simple_extent_dims'
/opt/aster/STA10.2/bibc/hdf/hdftsd.c:57: undefined reference to `H5Sclose'
/usr/bin/ld: Dwarf Error: Offset (97) greater than or equal to .debug_str size (45).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfclf.o): In function `hdfclf_':
/opt/aster/STA10.2/bibc/hdf/hdfclf.c:35: undefined reference to `H5Fclose'
/usr/bin/ld: Dwarf Error: Offset (524) greater than or equal to .debug_str size (254).
/opt/aster/STA10.2.x/lib/libasterd.a(hdftyp.o): In function `hdftyp_':
/opt/aster/STA10.2/bibc/hdf/hdftyp.c:58: undefined reference to `H5Giterate'
/opt/aster/STA10.2.x/lib/libasterd.a(hdftyp.o): In function `indiceType':
/opt/aster/STA10.2/bibc/hdf/hdftyp.c:78: undefined reference to `H5Gget_objinfo'
/usr/bin/ld: Dwarf Error: Offset (304) greater than or equal to .debug_str size (127).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfrsv.o): In function `hdfrsv_':
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:42: undefined reference to `H5Dget_type'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:43: undefined reference to `H5Dget_space'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:44: undefined reference to `H5Sget_simple_extent_ndims'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:45: undefined reference to `H5Sget_simple_extent_dims'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:48: undefined reference to `H5Dread'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:49: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:49: undefined reference to `H5T_STD_I32LE_g'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:49: undefined reference to `H5Tequal'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:49: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:49: undefined reference to `H5T_STD_I64LE_g'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:49: undefined reference to `H5Tequal'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:50: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:50: undefined reference to `H5T_STD_I32BE_g'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:50: undefined reference to `H5Tequal'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:50: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:50: undefined reference to `H5T_STD_I64BE_g'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:50: undefined reference to `H5Tequal'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:52: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:52: undefined reference to `H5T_NATIVE_LONG_g'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:52: undefined reference to `H5Tconvert'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:57: undefined reference to `H5Tclose'
/opt/aster/STA10.2/bibc/hdf/hdfrsv.c:60: undefined reference to `H5Sclose'
/usr/bin/ld: Dwarf Error: Offset (109) greater than or equal to .debug_str size (45).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfcld.o): In function `hdfcld_':
/opt/aster/STA10.2/bibc/hdf/hdfcld.c:35: undefined reference to `H5Dclose'
/usr/bin/ld: Dwarf Error: Offset (299) greater than or equal to .debug_str size (149).
/opt/aster/STA10.2.x/lib/libasterd.a(fetsco.o): In function `fetsco_':
/opt/aster/STA10.2/bibc/scotch/fetsco.c:37: undefined reference to `SCOTCH_graphInit'
/opt/aster/STA10.2/bibc/scotch/fetsco.c:40: undefined reference to `SCOTCH_graphBuild'
/opt/aster/STA10.2/bibc/scotch/fetsco.c:43: undefined reference to `SCOTCH_graphCheck'
/opt/aster/STA10.2/bibc/scotch/fetsco.c:46: undefined reference to `SCOTCH_archInit'
/opt/aster/STA10.2/bibc/scotch/fetsco.c:49: undefined reference to `SCOTCH_archCmplt'
/opt/aster/STA10.2/bibc/scotch/fetsco.c:52: undefined reference to `SCOTCH_stratInit'
/opt/aster/STA10.2/bibc/scotch/fetsco.c:55: undefined reference to `SCOTCH_graphMapInit'
/opt/aster/STA10.2/bibc/scotch/fetsco.c:58: undefined reference to `SCOTCH_graphMapCompute'
/opt/aster/STA10.2/bibc/scotch/fetsco.c:61: undefined reference to `SCOTCH_stratExit'
/opt/aster/STA10.2/bibc/scotch/fetsco.c:62: undefined reference to `SCOTCH_graphMapExit'
/opt/aster/STA10.2/bibc/scotch/fetsco.c:63: undefined reference to `SCOTCH_archExit'
/opt/aster/STA10.2/bibc/scotch/fetsco.c:64: undefined reference to `SCOTCH_graphExit'
/usr/bin/ld: Dwarf Error: Offset (257) greater than or equal to .debug_str size (127).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfwat.o): In function `hdfwat_':
/opt/aster/STA10.2/bibc/hdf/hdfwat.c:54: undefined reference to `H5Screate'
/opt/aster/STA10.2/bibc/hdf/hdfwat.c:55: undefined reference to `H5Sset_extent_simple'
/opt/aster/STA10.2/bibc/hdf/hdfwat.c:56: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfwat.c:56: undefined reference to `H5T_FORTRAN_S1_g'
/opt/aster/STA10.2/bibc/hdf/hdfwat.c:56: undefined reference to `H5Tcopy'
/opt/aster/STA10.2/bibc/hdf/hdfwat.c:57: undefined reference to `H5Tset_size'
/opt/aster/STA10.2/bibc/hdf/hdfwat.c:58: undefined reference to `H5Acreate'
/opt/aster/STA10.2/bibc/hdf/hdfwat.c:59: undefined reference to `H5Awrite'
/opt/aster/STA10.2/bibc/hdf/hdfwat.c:60: undefined reference to `H5Sclose'
/usr/bin/ld: Dwarf Error: Offset (744) greater than or equal to .debug_str size (460).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfwsv.o): In function `hdfwsv_':
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:76: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:76: undefined reference to `H5T_NATIVE_DOUBLE_g'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:78: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:78: undefined reference to `H5T_NATIVE_DOUBLE_g'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:81: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:81: undefined reference to `H5T_NATIVE_LONG_g'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:83: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:83: undefined reference to `H5T_NATIVE_INT_g'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:85: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:85: undefined reference to `H5T_NATIVE_HBOOL_g'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:87: undefined reference to `H5open'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:87: undefined reference to `H5T_FORTRAN_S1_g'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:99: undefined reference to `H5Tcopy'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:102: undefined reference to `H5Tset_size'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:103: undefined reference to `H5Tset_strpad'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:109: undefined reference to `H5Screate_simple'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:111: undefined reference to `H5Dcreate'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:113: undefined reference to `H5Dwrite'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:115: undefined reference to `H5Dclose'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:117: undefined reference to `H5Sclose'
/opt/aster/STA10.2/bibc/hdf/hdfwsv.c:120: undefined reference to `H5Tclose'
/usr/bin/ld: Dwarf Error: Offset (140) greater than or equal to .debug_str size (45).
/opt/aster/STA10.2.x/lib/libasterd.a(hdfcrg.o): In function `hdfcrg_':
/opt/aster/STA10.2/bibc/hdf/hdfcrg.c:62: undefined reference to `H5Gcreate'
collect2: ld returned 1 exit status

<E>_LINK_ERROR error during linking

<F>_UPDATE_FAILED Exception raised by AutoUpdate:
------------------------------------------------------------
Traceback:
Traceback (most recent call last):
File "/opt/aster/lib/python2.6/site-packages/asrun/maintenance.py", line 1301, in AutoUpdate
Update(run, num_update=num_update, *lpkg)
File "/opt/aster/lib/python2.6/site-packages/asrun/maintenance.py", line 1180, in Update
_build_aster(run, conf, True, REPREF, None, reptrav_built, lardv=lardv)
File "/opt/aster/lib/python2.6/site-packages/asrun/maintenance.py", line 898, in _build_aster
run.CheckOK()
File "/opt/aster/lib/python2.6/site-packages/asrun/run.py", line 714, in CheckOK
self.Sortie(4)
File "/opt/aster/lib/python2.6/site-packages/asrun/run.py", line 692, in Sortie
raise RunAsterError, exit_code
RunAsterError: 4

------------------------------------------------------------
Exit code : 4

---------------------------------------------------------------------------------
cpu system cpu+sys elapsed
---------------------------------------------------------------------------------
Download archives 0.23 0.10 0.33 21.87
Extraction of archives 0.27 0.07 0.34 0.37
Copy of updated files 0.12 0.14 0.26 0.38
Deletion of old files 0.33 0.60 0.93 1.02
Compilation in debug mode 6.77 1.75 8.52 6.62
Add object files to library 0.30 0.40 0.70 2.73
Build executables 2.31 0.89 3.20 4.66
---------------------------------------------------------------------------------
Total 10.36 3.96 14.32 37.71
---------------------------------------------------------------------------------

as_run 1.8.3

------------------------------------------------------------
--- DIAGNOSTIC JOB : <F>_UPDATE_FAILED
------------------------------------------------------------

Last edited by todd_alan_martin (2010-12-15 13:40:46)

mathieu.courtois · 2010-12-15 10:53:04

Hello,

I hope you kept the really STA10.2 !
How did you create STA10.2.x ?
You can compare the two config.txt files.

It seems that you don't link against the same libraries...

MC

todd_alan_martin · 2010-12-15 11:49:25

Hi

Yes. I kept the STA10.2, but it was giving abnormal abort errors, so I changed the ACML libraries from gfortran64_int64 to gfortran64. I then recompiled Metis, Mumps and Aster.

Should I have deleted /opt/aster and started again?

I created STA10.2.x by copying STA10.2 into a new folder, following the instructions outlined by JMB on the wiki.
http://www.code-aster.org/wiki/doku.php … tall:linux

Todd

Last edited by todd_alan_martin (2010-12-15 11:55:58)

todd_alan_martin · 2010-12-15 13:40:05

Hi.

I fixed this by deleting /opt/aster and starting again.
It seems the _int64 libraries didn't like my computer. Finally I have a working 10.2.29

Todd.

#1 2010-12-15 07:23:03

[SOLVED] Problem upgrading STA10.2

#2 2010-12-15 10:53:04

Re: [SOLVED] Problem upgrading STA10.2

#3 2010-12-15 11:49:25

Re: [SOLVED] Problem upgrading STA10.2

#4 2010-12-15 13:40:05

Re: [SOLVED] Problem upgrading STA10.2

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