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

todd_alan_martin
Member
Registered: 2008-03-06
Posts: 131

[SOLVED] Problem upgrading STA10.2

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)

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

mathieu.courtois
Administrator
From: France
Registered: 2007-11-21
Posts: 1,178

Re: [SOLVED] Problem upgrading STA10.2

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


Code_Aster release : last unstable on Ubuntu 16.04 64 bits - GNU Compilers

Please do not forget to tag your first post as *SOLVED* when it is!

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

todd_alan_martin
Member
Registered: 2008-03-06
Posts: 131

Re: [SOLVED] Problem upgrading STA10.2

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)

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

todd_alan_martin
Member
Registered: 2008-03-06
Posts: 131

Re: [SOLVED] Problem upgrading STA10.2

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.

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