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Hi

I tried setting LIBRARY_PATH, but it seemed to make no difference. I think
that this is the first time that I built the CellML API since a fresh Ubuntu
HH installation a few weeks ago, so I don't think the mixing of libraries
would be due to different versions of the CellML api libs.

It works fine with a similar DAE model.

I put both models on tracker item 1362.

Regards,
Randall

> -----Original Message-----
> From: cellml-tools-developers-bounces at cellml.org [mailto:cellml-tools-
> developers-bounces at cellml.org] On Behalf Of Andrew Miller
> Sent: Friday, 12 September 2008 10:18 a.m.
> To: A list for the developers of CellML tools
> Subject: Re: [cellml-dev] Can't get RunCellML going
>
> 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/b
> uild_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)[0xb7cfc
> 3dd]
> >
> >
> /home/rbri053/Now/CellMLapi/.libs/libcis.so.0(do_levmar+0xc6)[0xb7ce55b6]
> >
> >
> /tmp/3tpeCY6LKp8aiUOMXrDDLwLgY/generated.so(ComputeRates+0x80)[0xb7f7388
> 0]
> >
> >
> /home/rbri053/Now/CellMLapi/.libs/libcis.so.0(_ZN24CDA_CellMLIntegration
> Run9runthreadEv+0x1a5)[0xb7ce0c45]
> >
> >
> /home/rbri053/Now/CellMLapi/.libs/libcis.so.0(_ZN9CDAThread13start_routi
> neEPv+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
> >
> > ----------------------------------------------------------------------
> --
> >
> > _______________________________________________
> > cellml-tools-developers mailing list
> > cellml-tools-developers at cellml.org
> > http://www.cellml.org/mailman/listinfo/cellml-tools-developers
> >
>
> _______________________________________________
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> http://www.cellml.org/mailman/listinfo/cellml-tools-developers

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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

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