RE: Compiling on Linux-PPC970-Myrinet-MPI-xlC

From: Jordi Camps (
Date: Thu Mar 10 2005 - 18:08:02 CST


Thank you very much for your fast answer. The define worked, and the
compilation process advanced until it hit the CollectionMaster.C file. Now,
when I'm compiling I get the following error:
        ~/MD/NAMD/NAMD_2.5_Source/Linux-PPC-MPI-xlC $ mpicxx -w
-I.rootdir/charm-5.8/mpi-linux-gm2-xlc64/include -DCMK_OPTIMIZE=1 -Isrc
-o obj/CollectionMaster.o -c src/CollectionMaster.C
        "/usr/include/g++/cstdio", line 108.9: 1540-0130 (S) "::fgetpos" is
not declared.
        "/usr/include/g++/cstdio", line 110.9: 1540-0130 (S) "::fopen" is
not declared.
        "/usr/include/g++/cstdio", line 115.9: 1540-0130 (S) "::freopen" is
not declared.
        "/usr/include/g++/cstdio", line 118.9: 1540-0130 (S) "::fsetpos" is
not declared.
        "/usr/include/g++/cstdio", line 137.9: 1540-0130 (S) "::tmpfile" is
not declared.
        "src/CollectionMaster.C", line 105.24: 1540-0274 (S) The name lookup
for "fopen" did not find a declaration.
        "/usr/include/g++/cstdio", line 63.8: 1540-2407 (I) The local macro
"fopen" is not visible in the current source.

This seems to be a problem with the system libraries, but I think that this
is quite improbable. Maybe a problem with the include paths :-? Do you have
some clue?


Jordi Camps Puchades
Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
c/. Jordi Girona 1-3              
Modul C6-E201                     Tel.  : 934 011 650
E-08034 Barcelona                 Fax   : 934 017 014
Catalunya (Spain)                 e-mail:
-----Mensaje original-----
De: Gengbin Zheng [] 
Enviado el: jueves, 10 de marzo de 2005 22:55
Para: Brian Bennion
CC: Jordi Camps;
Asunto: Re: namd-l: Compiling on Linux-PPC970-Myrinet-MPI-xlC
Just a small correction:
The latest NAMD in cvs repository should have this fixed.
Brian Bennion wrote:
>Quickly, just block strstream.h from being searched for, its not 
>ie in the arch file
>On Thu, 10 Mar 2005, Jordi Camps wrote:
>>Hello everybody,
>>I'm trying to compile NAMD on a cluster of PPC970 (G5) processors 
>>connected through a Myrinet and using a SuSe Linux 2.6.5 as operating 
>>system. The compiler set that I want to use is the IBM compilers: xlc, 
>>xlC, *_r...
>>At this first stage I'm trying to compile only the basic NAMD: no 
>>fftw, no tcl, no plugins.
>>I updated the charm++ to the last version (5.8) and it compiled OK and 
>>passed megatest tests with up to 16 processors (8 nodes).
>>But when I try to compile the NAMD, I get some errors. The process 
>>followed to compile NAMD has been this:
>>	Update Make.charm
>>	Create files Linux-PPC-MPI-xlC.arch & Linux-PPC-MPI-xlC.base (.fftw,
>>.tcl & .plugins coming soon ;-))
>>	./config Linux-PPC-MPI-xlC
>>	cd Linux-PPC-MPI-xlC
>>	make
>>But the first lines say this:
>>	mkdir inc
>>	mkdir obj
>>	mpicxx -w -DSOCKLEN_T=size_t 
>>-I.rootdir/charm-5.8/mpi-linux-gm2-xlc64/include -DCMK_OPTIMIZE=1 
>>-Isrc -Iinc -DNAMD_VERSION=\"2.5\" 
>>-DNAMD_PLATFORM=\"Linux-PPC-MPI-xlC-MPI\"  -O3 -o obj/common.o -c
>>	"src/InfoStream.h", line 17.10: 1540-0836 (S) The #include file 
>><strstream.h> is not found.
>>	make: *** [obj/common.o] Error 1
>>If I edit the InfoStream.h file and change <strstream.h> to 
>><strstream> I get another bunch of messages like:
>>	"src/common.C", line 218.3: 1540-0256 (I) A parameter of type 
>>"std::basic_ostream<char,std::char_traits<char> > &" cannot be 
>>initialized with an expression of type "infostream".
>>	"src/InfoStream.h", line 67.13: 1540-1283 (I) "operator<<(infostream
>>&, const Vector &)" is not a viable candidate."
>>Someone has compiled NAMD with xlC? Someone can help me?
>>Thanks in advance.
>>Jordi Camps Puchades
>>Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2 
>>UPC-CIRI c/. Jordi Girona 1-3
>>Modul C6-E201                     Tel. : 934 011 650
>>E-08034 Barcelona                 Fax  : 934 017 014
>>Catalunya (Spain)                 e-mail:
>  Brian Bennion, Ph.D.
>  Bioscience Directorate
>  Lawrence Livermore National Laboratory
>  P.O. Box 808, L-448
>  7000 East Avenue       phone: (925) 422-5722
>  Livermore, CA  94550   fax:   (925) 424-6605

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:18:38 CST