AMBER Archive (2008)

Subject: Re: AMBER: Problems installing Amber Tools for Amber 10

From: Sam Danziger (sam.danziger_at_gmail.com)
Date: Fri May 16 2008 - 12:06:05 CDT

David,

Thanks for the response, I was starting to fear that my problem had
dissapeared into the great beyond.

Here is the gcc 4.3.0 error message. Note: I had to change to
gfortran and not compile mopac to get this far.

Thank you,
-Sam

gcc -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajecto
ry.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o experimental.o
 ptraj.o actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o /extra/p53
0/software/amber10/lib/libpdb.a /extra/p530/software/amber10/lib/libsym.a /extra
/p530/software/amber10/lib/arpack.a /extra/p530/software/amber10/lib/lapack.a /e
xtra/p530/software/amber10/lib/blas.a /extra/p530/software/amber10/lib/f2c.a
../netcdf/lib/libnetcdf.a -lm
/extra/p530/software/amber10/lib/libpdb.a(pdb_read.o): In function `pdb_read_str
ing.':
pdb_read.c:(.text+0x1d32): undefined reference to `_intel_fast_memset'
/extra/p530/software/amber10/lib/libpdb.a(pdb_sscanf.o): In function `pdb_sscanf
':
pdb_sscanf.c:(.text+0x2a0): undefined reference to `_intel_fast_memset'
/extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `pdb_sprint
f':
pdb_sprntf.c:(.text+0x2b9): undefined reference to `_intel_fast_memset'
pdb_sprntf.c:(.text+0x4de): undefined reference to `_intel_fast_memset'
pdb_sprntf.c:(.text+0x7ea): undefined reference to `_intel_fast_memset'
/extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `outexp':
pdb_sprntf.c:(.text+0xbab): undefined reference to `__intel_f2int'
pdb_sprntf.c:(.text+0xbd7): undefined reference to `__intel_f2int'
pdb_sprntf.c:(.text+0xd4a): undefined reference to `_intel_fast_memset'
/extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `outfloat':

pdb_sprntf.c:(.text+0xdd7): undefined reference to `__intel_f2int'
pdb_sprntf.c:(.text+0xe09): undefined reference to `_intel_fast_memset'
pdb_sprntf.c:(.text+0xf91): undefined reference to `_intel_fast_memcpy'
pdb_sprntf.c:(.text+0x100d): undefined reference to `_intel_fast_memset'
pdb_sprntf.c:(.text+0x1033): undefined reference to `_intel_fast_memset'
/extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `outstr':
pdb_sprntf.c:(.text+0x1151): undefined reference to `_intel_fast_memcpy'
pdb_sprntf.c:(.text+0x119b): undefined reference to `_intel_fast_memset'
/extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `outunsigne
d':
pdb_sprntf.c:(.text+0x12a7): undefined reference to `_intel_fast_memset'
/extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `outint':
pdb_sprntf.c:(.text+0x13f7): undefined reference to `_intel_fast_memset'
collect2: ld returned 1 exit status
make[1]: *** [rdparm] Error 1
make[1]: Leaving directory `/extra/p530/software/amber10/src/ptraj'
make: *** [install] Error 2

On Thu, May 15, 2008 at 9:47 PM, David A. Case <case_at_scripps.edu> wrote:
> On Mon, May 12, 2008, Sam Danziger wrote:
>
>> I've tried to install Amber Tools 1.0, but get an error message when I
>> try to compile.
>>
>> I'm using Gentoo linux (Linux version 2.6.22-gentoo-r18), and have
>> tried gcc 3.4.1, 3.4.4 and 4.3.0 (4.3.0 gives me a different error
>> than below).
>>
>
> Thanks for the report; aren't C++ error messages awe-inspiring sometimes?
>
> I've entered this into bugzilla. Probably no developer has used Gentoo,
> although other Linux and Mac and cygwin versions of gcc seem OK here.
>
> It might be helpful to post the 4.3.0 error message as well...you never know
> when a clue will pop up.
>
> ...regards...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
Samuel A. Danziger
Dept. of Biomedical Engineering
PhD Candidate
University of California
Irvine, CA 92697
sdanzige_at_uci.edu
(908)246-4502
http://samdanziger.com/

Associated Graduate Students
VP Financial Affairs
vpfinance_at_ags.uci.edu

Truth Cannot Contradict Truth
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu