Re: AMBER: parallel AMBER/pmemd installation problem on Opteron

From: Robert Duke <rduke.email.unc.edu>
Date: Wed, 23 Feb 2005 08:17:54 -0500

Jyh-Shyong -
I just hit and fixed this one while porting pmemd to a cray with opteron
cpu's and a pgi compiler. Seems the pgi compiler is extra picky, or
interprets variable scope nesting restrictions a bit differently. A diff
file of the fix is:

3431c3431
< integer ierr_nmr

---
> integer ierr
3472c3472
< call opnmrg(redir(6)(1:iredir(6)), idumpu, 0, iout, ierr_nmr)
---
> call opnmrg(redir(6)(1:iredir(6)), idumpu, 0, iout, ierr)
(basically, change ierr to ierr_nmr in lines 3431 and 3472 of nmr_calls.f90
I'll get a patch for this up on the amber web site, but a hand fix should be 
pretty easy, aside from the fact that a patch has already been applied for 
another problem in nmr_calls.f90, so the line numbers may be different.  I 
will send you the entire file separately so we can quickly dodge that 
complexity.
Regards - Bob Duke
----- Original Message ----- 
From: "Jyh-Shyong Ho" <c00jsh00.nchc.org.tw>
To: <amber.scripps.edu>
Sent: Wednesday, February 23, 2005 12:08 AM
Subject: AMBER: parallel AMBER/pmemd installation problem on Opteron
> Dear Amber users,
>
> After applied all bugfixes,  I failed to install the parallel veriosn of 
> PMEMD
> with pgf90 and mpich.  Here is file config.h I used:
>
> #!/bin/csh -f
> setenv MPICH_HOME /opt/mpich/ch_p4.pgi
> setenv MPICH_INCLUDE $MPICH_HOME/include
> setenv MPICH_LIBDIR $MPICH_HOME/lib
> setenv MPILIB "-L$MPICH_LIBDIR -lmpich"
>
> setenv PREPROCFLAGS "-DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_VECT_OPT"
>
> setenv CPP "/lib/cpp -traditional  -I$MPICH_INCLUDE"
>
> setenv OPT_LO  "pgf90 -c -fast"
> setenv OPT_MED "pgf90 -c -fast -O3"
> setenv OPT_HI  "pgf90 -c -fastsse -Mipa=fast,inline -O3"
>
> setenv LOAD "pgf90 -fastsse -Mipa=fast,inline "
> setenv LOADLIB " $MPILIB"
>
>
> And the last part of compilation error message is:
> ...
> cd src; make install
> make[1]: Entering directory `/package/amber8/src/pmemd/src'
> ../Compile OPT_HI -P  nmr_calls.f90
> cat nmr_calls.f90 | 
> /lib/cpp -traditional  -I/opt/mpich/ch_p4.pgi/include -P   -DMPI -DSLOW_NONBLOCKING_MPI 
>  -DDIRFRC_VECT_OPT  > _nmr_calls_.f90
> pgf90 -c -fastsse -Mipa=fast,inline -O3 _nmr_calls_.f90
> PGF90-S-0155-ierr is use associated and cannot be redeclared 
> (_nmr_calls_.f90: 3492)
>  0 inform,   0 warnings,   1 severes, 0 fatal for nmrnrg
> PGF90/any Linux/x86-64 5.2-4: compilation completed with severe errors
> make[1]: *** [nmr_calls.o] Error 1
> make[1]: Leaving directory `/package/amber8/src/pmemd/src'
> make: *** [install] Error 2
>
>
> Files from PGI's resource page 
> http://www.pgroup.com/resources/amber/amber8_pgi52.htm
> are used for  making file config.h.
>
> Any idea?
>
> By the way, has anyone installed AMBER8 serial and parallel version 
> successfully
> on HP Superdome running HPUX?
>
> Best regards
>
> Jyh-Shyong Ho, Ph.D.
> Research Scientist
> National Center for High Performance Computing
> Hsinchu, Taiwan, ROC
>
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Received on Wed Feb 23 2005 - 13:53:03 PST