AMBER Archive (2004)

Subject: Re: AMBER: Running on MPI

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Oct 13 2004 - 08:59:38 CDT

I don't have any experiences with Opteron compiling, that's why I suggested
that link on the AMBER page. You might have to upgrade to AMBER8.
Old versions of amber can't always be easily compiled on every system,
sometimes the code needed lots of changes to be compatible with different
compilers, etc. You can upgrade or try to work through all of the problems.

Maybe someone else has compiled AMBER7 on an Opteron and can share
a MACHINE file and their experience.
Carlos

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Wu Yingliang wrote:

>Dear Prof. Carlos L. Simmerling,
>
>Thanks a lot for your warm-hearted reply!
>
>Recent days, I try my best to install AMBER 7 again, however, I can not succeed too.
>
>I have read the "Running Amber on AMD opteronshttp://amber.scripps.edu/opteron.html", however, there is no config.h file in amber7. I also do not know to use it if I add it in the amber7 or amber7/src directory.
>
>Now, the wrong messages are as following:
>
>**************************************
>
>cd src
>make install
>
>....
>
>cd lib; make install
>make[1]: Entering directory `/home/wxli/amber7/src/lib'
>./Compile L0 -P -DNEWPARM nxtsec.f
>cat nxtsec.f | /lib/cpp -traditional -P
>-DNEWPARM -DLinux -DMPI > _nxtsec_.f
>pgf77 -c -g -tp k8-64 -Mnoframe
>-Msecond_underscore _nxtsec_.f
>./Compile LOAD -o new2oldparm new2oldparm.o nxtsec.o
>pgf77 -o new2oldparm new2oldparm.o nxtsec.o -lmmv new2oldparm ../../exe
>make[1]: Leaving directory `/home/wxli/amber7/src/lib'
>
>cd addles; make install
>make[1]: Entering directory `/home/wxli/amber7/src/addles'
> cd ../lib; ./Makelist ../lib/random.o ../lib/mexit.o ../lib/nxtsec.o
> make[2]: Entering directory `/home/wxli/amber7/src/lib'
> ../Compile L2 -P -DDPREC -o random.o random.f
> cat random.f | /lib/cpp -traditional -P -DDPREC -DLinux -DMPI > _random_.f
> No more processes.
> make[2]: *** [random.o] Error 1
> make[2]: Leaving directory `/home/wxli/amber7/src/lib'
> make[1]: *** [libobj] Error 1
> make[1]: Leaving directory `/home/wxli/amber7/src/addles'
> make: *** [install] Error 2
>
>
>...
>
>**********************************************
>
>Wrong messages indicate that programe can not find file "random.o" during making install after "cd addles". However, If I direct do "/Compile L2 -P -DDPREC -o random.o random.f" in the directory of amber7/src/lib, Then this wrong message will disappear, however, other wrong messages come too.
>
>We suspect there is something wrong for file "Makefile" or other places, right?
>
>
>Looking forward to your help once more!
>
>Highly Thank you very much in advance!
>
>
>Best wishes,
>
>Yingliang Wu
>
>
>
>
>
>
>
>>======================================================================
>>　　have you read and followed the Opteron compiling instructions
>>on the AMBER web page?
>>http://amber.scripps.edu/opteron.html
>>
>>
>
>
>
>>>wish_71 wrote:
>>>
>>>
>
>
>
>>>Dear Prof. Carlos L. Simmerling,
>>>
>>>Thanks a lot for your reply!
>>>
>>>The processes are AMD Opteron 244. Before we make install, we just modifer P6 bythe K8-64 in the MACHINE file. The wrong messages are as following through using Machine.pgf77_mpi:
>>>
>>>=============================================================
>>>
>>>1004.html)
>>>
>>>
>>>
>>>
>
>
>
>
>
>
>　　　　　　　
>2004-10-13
>=======================================
>College of Life Science
>Wuhan Univeristy
>Wuhan, China
>Email: wuyliang_at_public.wh.hb.cn
>=======================================
>
>
>
>
>
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