AMBER Archive (2005)

Subject: Re: AMBER: Leap compilation issues

From: justin litchfield (litch_at_stanford.edu)
Date: Mon Jul 11 2005 - 01:49:33 CDT

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_at_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_at_jd10 test]# export LD_LIBRARY_PATH=/opt/intel/ifc/lib
at which point i get this

[root_at_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_at_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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