AMBER Archive (2005)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed Feb 23 2005 - 07:17:54 CST


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_at_nchc.org.tw> To: <amber_at_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 > > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber_at_scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu