4.3.0 update:
I checked the lib directory and found that the copy of
libpdb.a
was two days old, although all of the other .a's were recently regenerated.
I deleted libpdb.a and then reran make -f Makefile_at.
It looks like Amber Tools compiled and installed correctly after that,
although this is without any of the fortran parts as 4.3.0 does not
include g77.
-Sam
On Fri, May 16, 2008 at 10:06 AM, Sam Danziger <sam.danziger.gmail.com> wrote:
> 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.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.scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo.scripps.edu
>>
>
>
>
> --
> Samuel A. Danziger
> Dept. of Biomedical Engineering
> PhD Candidate
> University of California
> Irvine, CA 92697
> sdanzige.uci.edu
> (908)246-4502
> http://samdanziger.com/
>
> Associated Graduate Students
> VP Financial Affairs
> vpfinance.ags.uci.edu
>
> Truth Cannot Contradict Truth
>
--
Samuel A. Danziger
Dept. of Biomedical Engineering
PhD Candidate
University of California
Irvine, CA 92697
sdanzige.uci.edu
(908)246-4502
http://samdanziger.com/
Associated Graduate Students
VP Financial Affairs
vpfinance.ags.uci.edu
Truth Cannot Contradict Truth
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun May 18 2008 - 06:07:51 PDT
