AMBER Archive (2005)

Subject: Re: AMBER: Compile question??

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Jun 06 2005 - 09:32:06 CDT

Anthony -
One final thought. Do a "man cpu_time" on your system. My old 7.3 compiler
man pages report cpu_time as an intrinsic; ie. no need to link in anything.
Your man page may tell you what you need to link in for the implementation
of cpu_time that comes with the 7.0 compiler. If you don't have man pages,
you would have to install them, or plow through the manuals that came with
your compiler version.
Regards - Bob

----- Original Message -----
From: "Anthony Cruz" <acb15885_at_uprm.edu>
To: <amber_at_scripps.edu>
Sent: Monday, June 06, 2005 9:24 AM
Subject: Re: AMBER: Compile question??

>I used configure sgi_mips f90 mpi and this is my config.h.
> -------------------- config.h -------------------------------
> #!/bin/csh -f
> setenv PREPROCFLAGS "-DMPI -DDIRFRC_VECT_OPT"
> setenv CPP /lib/cpp
>
> # SGI specific ``code'' to recognize the type of machine and its
> environment
> set cpuarch = ` hinv -t cpu | awk ' { print $3 } ' | head -1 `
>
> # Do we have the FFT libraries in libcomplib.sgimath.a?
> if ( -e /usr/lib/libcomplib.sgimath.a | \
> -e /usr/lib32/mips4/libcomplib.sgimath.a | \
> -e /usr/lib32/mips4/libcomplib.sgimath.so | \
> -e /usr/lib64/mips4/libcomplib.sgimath.a ) then
> setenv PREPROCFLAGS "$PREPROCFLAGS -DSGIFFT"
> set sgimathlib = "-lcomplib.sgimath "
> endif
>
> if ( $cpuarch == R8000) then
> set mipsflag = "-mips4 -n32 -r8000 "
> set nflags = (-WK,-dr=AKC -OPT:cis=off:roundoff=3:IEEE_arithmetic=3
> -SWP:strict_ivdep=OFF -TENV:X=3 )
> else
> if ($cpuarch == R10000) then
> set mipsflag = -r10000
> else if ($cpuarch == R12000) then
> set mipsflag = -r10000
> else if ($cpuarch == R14000) then
> set mipsflag = -r14000
> else if ($cpuarch == R16000) then
> set mipsflag = -r16000
> else
> echo "Error - unsupported SGI CPU type $cpuarch!"
> exit(1)
> endif
> set mipsflag = "$mipsflag -mips4 -n32"
> set nflags = ( -OPT:roundoff=3:IEEE_arithmetic=3:fast_bit_intrinsics=ON )
> endif
>
> setenv CC "cc $mipsflag"
> setenv CFLAGS "-O3 $nflags "
>
> setenv OPT_LO "f90 -nocpp $mipsflag -c -O1 -old_rl $nflags "
> setenv OPT_MED "f90 -nocpp $mipsflag -c -O3 -old_rl $nflags "
> setenv OPT_HI "f90 -nocpp $mipsflag -c -O3 -old_rl $nflags "
>
> setenv LOAD "f90 $mipsflag "
> setenv LOADLIB " $sgimathlib -lfastm -lmpi"
>
> Best wishes,
> Anthony
>
> On Monday 06 June 2005 8:38 am, Robert Duke wrote:
>> This is known to work for version 7.4.3, and I have no reason to suspect
>> difficulties with earlier versions (I am basically sure that we have
>> built
>> with earlier versions, but as the compilers on various platforms have
>> been
>> upgraded over the last year or two, I am not sure how far back in the
>> mips
>> f90 compiler line we go). The call you are not linking to is an f90
>> intrinsic, cpu_time(). I suspect you did not do the pmemd configure
>> correctly and are invoking some other compiler or the fortran compiler in
>> another mode (f77) but of course don't know. What does your config.h in
>> the pmemd directory look like? It should have been built there using
>> './configure sgi_mips f90 mpi'. Could you possibly have a problem with
>> the
>> f90 installation (missing libraries for the intrinsics, or stuff in the
>> wrong place)?
>> Regards - Bob Duke
>>
>> ----- Original Message -----
>> From: "Anthony Cruz" <acb15885_at_uprm.edu>
>> To: <amber_at_scripps.edu>
>> Sent: Monday, June 06, 2005 7:59 AM
>> Subject: AMBER: Compile question??
>>
>> > Can pmemd be compiled with MipsPro 7.2.1 to run in parallel? I am
>> > having
>> > problems compiling the parallel version of pmemd. It gives the
>> > following
>> > error:
>> > ld32: ERROR 33: Unresolved text symbol "cpu_time_" -- 1st referenced by
>> > pmemd_lib.o.
>> > Use linker option -v to see when and which objects, archives and
>> > dsos
>> > are loaded.
>> > ld32: INFO 152: Output file removed because of error.
>> > *** Error code 1 (bu21)
>> > *** Error code 1 (bu21)
>> >
>> > --
>> > Best wishes,
>> > Anthony
>> > -----------------------------------------------------------------------
>> > The AMBER Mail Reflector
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>
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