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- From: ak.miller at auckland.ac.nz (Andrew Miller)
- Subject: [cellml-dev] Can't get RunCellML going
- Date: Fri, 12 Sep 2008 10:18:20 +1200
Randall Britten wrote:
>
> Hi
>
> Not sure whether I am missing something obvious, let me know. If not,
> I?ll make a tracker item for this:
>
> Note CellML2C is fine, and ?make check? finds no errors.
>
> With revision 2638, when I do a clean checkout and a make (as
> described in
> https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/docs/build_process_kubuntu_7_10.txt
>
> ), and then try to run RunCellML on a CellML file, there seems to be a
> link problem:
>
> /usr/bin/ld: cannot find -lcis
>
> collect2: ld returned 1 exit status
>
> Tried export LD_LIBRARY_PATH=.libs, but still got same problem.
>
Hi Randall,
You also need to set LIBRARY_PATH so ld knows where to find the
libraries to compile against.
>
> Also tried ?make install?, which resulted in a lot of cellml .so?s in
> /usr/local/lib,
>
> Setting LD_LIBRARY_PATH to /usr/local/lib, and trying again:
>
> Trying that results in a huge text output.
>
> $ ./RunCellML ../DAEsModel/SimpleDAE_NonLinear4.cellml > errors.txt 2>&1
>
It looks like you may be mixing library versions... but if not this is
of concern. Does it only occur with one particular model?
> *** glibc detected *** /home/rbri053/Now/CellMLapi/.libs/lt-RunCellML:
> free(): invalid pointer: 0x0804c3f0 ***
>
> ======= Backtrace: =========
>
> /lib/tls/i686/cmov/libc.so.6[0xb7af3a85]
>
> /lib/tls/i686/cmov/libc.so.6(cfree+0x90)[0xb7af74f0]
>
> /home/rbri053/Now/CellMLapi/.libs/libcis.so.0(dAx_eq_b_LU_noLapack+0x36b)[0xb7cfb90b]
>
> /home/rbri053/Now/CellMLapi/.libs/libcis.so.0(dlevmar_dif+0x8fd)[0xb7cfc3dd]
>
> /home/rbri053/Now/CellMLapi/.libs/libcis.so.0(do_levmar+0xc6)[0xb7ce55b6]
>
> /tmp/3tpeCY6LKp8aiUOMXrDDLwLgY/generated.so(ComputeRates+0x80)[0xb7f73880]
>
> /home/rbri053/Now/CellMLapi/.libs/libcis.so.0(_ZN24CDA_CellMLIntegrationRun9runthreadEv+0x1a5)[0xb7ce0c45]
>
> /home/rbri053/Now/CellMLapi/.libs/libcis.so.0(_ZN9CDAThread13start_routineEPv+0x11)[0xb7ce4541]
>
> /lib/tls/i686/cmov/libpthread.so.0[0xb79304fb]
>
> /lib/tls/i686/cmov/libc.so.6(clone+0x5e)[0xb7b5ee5e]
>
> ======= Memory map: ========
>
> 08048000-0804b000 r-xp 00000000 08:08 129637
> /home/rbri053/Now/CellMLapi/.libs/lt-RunCellML
>
> 0804b000-0804c000 rw-p 00003000 08:08 129637
> /home/rbri053/Now/CellMLapi/.libs/lt-RunCellML
>
> 0804c000-080cd000 rw-p 0804c000 00:00 0 [heap]
>
> b6d00000-b6d21000 rw-p b6d00000 00:00 0
>
> b6d21000-b6e00000 ---p b6d21000 00:00 0
>
> b6e8e000-b6e8f000 ---p b6e8e000 00:00 0
>
> b6e8f000-b7691000 rw-p b6e8f000 00:00 0
>
> b7691000-b76a5000 r-xp 00000000 08:06 796692 /usr/lib/libz.so.1.2.3.3
>
> b76a5000-b76a6000 rw-p 00013000 08:06 796692 /usr/lib/libz.so.1.2.3.3
>
> b76a6000-b787a000 r-xp 00000000 08:06 798951 /usr/lib/libgsl.so.0.10.0
>
> b787a000-b7884000 rw-p 001d3000 08:06 798951 /usr/lib/libgsl.so.0.10.0
>
> b7884000-b7886000 r-xp 00000000 08:06 319641
> /lib/tls/i686/cmov/libdl-2.7.so
>
> b7886000-b7888000 rw-p 00001000 08:06 319641
> /lib/tls/i686/cmov/libdl-2.7.so
>
> b7888000-b7893000 r-xp 00000000 08:08 129567
> /home/rbri053/Now/CellMLapi/.libs/libannotools.so.0.0.0
>
> b7893000-b7894000 rw-p 0000a000 08:08 129567
> /home/rbri053/Now/CellMLapi/.libs/libannotools.so.0.0.0
>
> b7894000-b7896000 rw-p b7894000 00:00 0
>
> b7896000-b78a7000 r-xp 00000000 08:08 129579
> /home/rbri053/Now/CellMLapi/.libs/libcevas.so.0.0.0
>
> b78a7000-b78a9000 rw-p 00010000 08:08 129579
> /home/rbri053/Now/CellMLapi/.libs/libcevas.so.0.0.0
>
> b78a9000-b78d3000 r-xp 00000000 08:08 129573
> /home/rbri053/Now/CellMLapi/.libs/libcuses.so.0.0.0
>
> b78d3000-b78d4000 rw-p 00029000 08:08 129573
> /home/rbri053/Now/CellMLapi/.libs/libcuses.so.0.0.0
>
> b78d4000-b78d5000 rw-p b78d4000 00:00 0
>
> b78d5000-b78fa000 r-xp 00000000 08:08 129585
> /home/rbri053/Now/CellMLapi/.libs/libmalaes.so.0.0.0
>
> b78fa000-b78fb000 rw-p 00025000 08:08 129585
> /home/rbri053/Now/CellMLapi/.libs/libmalaes.so.0.0.0
>
> b78fb000-b78fc000 rw-p b78fb000 00:00 0
>
> b78fc000-b7928000 r-xp 00000000 08:08 129592
> /home/rbri053/Now/CellMLapi/.libs/libccgs.so.0.0.0
>
> b7928000-b792a000 rw-p 0002b000 08:08 129592
> /home/rbri053/Now/CellMLapi/.libs/libccgs.so.0.0.0
>
> b792a000-b792b000 rw-p b792a000 00:00 0
>
> b792b000-b793f000 r-xp 00000000 08:06 319654
> /lib/tls/i686/cmov/libpthread-2.7.so
>
> b793f000-b7941000 rw-p 00013000 08:06 319654
> /lib/tls/i686/cmov/libpthread-2.7.so
>
> b7941000-b7944000 rw-p b7941000 00:00 0
>
> b7944000-b7a5d000 r-xp 00000000 08:06 798784 /usr/lib/libxml2.so.2.6.31
>
> b7a5d000-b7a62000 rw-p 00119000 08:06 798784 /usr/lib/libxml2.so.2.6.31
>
> b7a62000-b7a63000 rw-p b7a62000 00:00 0
>
> b7a63000-b7a86000 r-xp 00000000 08:06 319642
> /lib/tls/i686/cmov/libm-2.7.so
>
> b7a86000-b7a88000 rw-p 00023000 08:06 319642
> /lib/tls/i686/cmov/libm-2.7.so
>
> b7a88000-b7bd1000 r-xp 00000000 08:06 319637
> /lib/tls/i686/cmov/libc-2.7.so
>
> b7bd1000-b7bd2000 r--p 00149000 08:06 319637
> /lib/tls/i686/cmov/libc-2.7.so
>
> b7bd2000-b7bd4000 rw-p 0014a000 08:06 319637
> /lib/tls/i686/cmov/libc-2.7.so
>
> b7bd4000-b7bd7000 rw-p b7bd4000 00:00 0
>
> b7bd7000-b7be1000 r-xp 00000000 08:06 319551 /lib/libgcc_s.so.1
>
> b7be1000-b7be2000 rw-p 0000a000 08:06 319551 /lib/libgcc_s.so.1
>
> b7be2000-b7cca000 r-xp 00000000 08:06 795949 /usr/lib/libstdc++.so.6.0.9
>
> b7cca000-b7ccd000 r--p 000e8000 08:06 795949 Aborted
>
> ------------------------------------------------------------------------
>
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>
- [cellml-dev] Can't get RunCellML going, Randall Britten, 09/12/2008
- [cellml-dev] Can't get RunCellML going, Andrew Miller, 09/12/2008
- [cellml-dev] Can't get RunCellML going, Randall Britten, 09/15/2008
- [cellml-dev] Can't get RunCellML going, Andrew Miller, 09/12/2008
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