Is the path /opt/intel/ifc/lib the correct compiler version? The reason I
ask is that Intel switched to the name ifort for version 8 and later. Hence
I suspect you may be setting LD_LIBRARY_PATH to a different compiler version
to the one you compiled with.
There are two options:
1. Re-run amber's configure script with the -static option and then
recompile.
2. Make sure you source /opt/intel_fc_80/bin/ifortvars.sh -> Or the correct
path for your compiler version. BEFORE you compile and BEFORE you run
Amber... Alternatively add this to your .bashrc file.
All the best
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of justin litchfield
> Sent: Sunday, July 10, 2005 23:50
> To: amber.scripps.edu
> Subject: Re: AMBER: Leap compilation issues
>
> i am definitely not very informed on these matters, but was able to
> get leap working. i just had to install one more X11-dev
> library. i
> did get everything compiled using ifc8.1. i got ifc 9.0 and found a
> thread that talks about how one can manually install the 64-bit
> compilers, but i don't have the expertise to get that to work that
> really. i'm a bit over my head here. i'm not really sure about
> which parts were 64 bit and which are 32 bit. xleap and tleap both
> seem to work, but sander seems to be broken. the first error was
>
> [root.jd10 test]# make test
> cd dmp; ./Run.dmp
> ../../exe/sander: error while loading shared libraries: libsvml.so:
> cannot open shared object file: No such file or directory
> ./Run.dmp: Program error
> make: *** [test.sander.no_lmod] Error 1
>
> so i googled that problem and found that this could be fixed
> by doing
> this:
> [root.jd10 test]# export LD_LIBRARY_PATH=/opt/intel/ifc/lib
> at which point i get this
>
> [root.jd10 test]# make test
> cd dmp; ./Run.dmp
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> sander 0814EE20 Unknown Unknown Unknown
> sander 08077776 Unknown Unknown Unknown
> sander 0804A398 Unknown Unknown Unknown
> Unknown 00449DE6 Unknown Unknown Unknown
> sander 0804A251 Unknown Unknown Unknown
> ./Run.dmp: Program error
> make: *** [test.sander.no_lmod] Error 1
> [root.jd10 test]#
>
> sorry if this is jumbled or confusing. at least this is excititg,
> and i got leap working. i'll keep working on this. thank you all,
>
> justin
>
>
> On Jul 10, 2005, at 10:13 PM, David A. Case wrote:
>
> > On Sun, Jul 10, 2005, justin litchfield wrote:
> >
> >
> >> i am now trying to install amber on a new Athlon 64 running FC4.
> >> everything seems to go great, i'm using gcc 4, ifc 8.1, but when it
> >> gets to the leap installation it crashes out.
> >>
> >
> >
> >> MapAg.c:190: warning: cast from pointer to integer of
> different size
> >> MapAg.c:209: warning: cast from pointer to integer of
> different size
> >>
> >
> >
> >> WcActCB.c:1536: error: syntax error before ???}??? token
> >> WcActCB.c:1538: error: syntax error before ???(??? token
> >>
> >
> > I know this is question that mainly reflects by ignorance, but is
> > "Athlon 64
> > running FC4" a 64-bit OS (where pointers are 64-bit). xleap is
> > probably
> > broken on such a platform. See the comments in $AMBERHOME/src/
> > Makefile
> > on how to compile for tleap only (which seems to be 64-bit clean).
> >
> > If any amber users know the answers to the following questions,
> > please post
> > them:
> >
> > 1. Has anyone gotten xleap to run in 64-bit mode? How?
> >
> > 2. Are there compile/load options that can force a 32-bit build?
> >
> > 3. If you take an xLeap executable from an IA-32 machine, and try
> > to run it
> > on a 64-bit machine, will it work?
> >
> > 4. Has anyone used gcc 4 to compiler xaLeap on a 32-bit system?
> >
> > 5. Has anyone every seriously looked a compiler warnings
> like those
> > cited
> > above, and thought about whether things could be fixed?
> >
> > ...thanks!....dac
> >
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>
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Received on Mon Jul 11 2005 - 18:53:01 PDT
