Re: AMBER: Compiler issues with Altix450

From: <>
Date: Mon, 10 Mar 2008 16:45:37 -0400 (EDT)

I have been able to compile to some degree after locating the icc compiler. However, compilation of the leap program hangs up due to the lack of an /usr/X11/IntrinsicP.h file needed for compilation of the WcActCB.c program. This IntrinsicP.h file is indeed absent from the /usr/X11 directory.

What is the best solution to this problem? Is there a IntrinsicP.h file I can get somehow? Or is there a problem generating this file?

John Finke

The compiler error is listed below:

cd leap; make install
make[1]: Entering directory `/home/jfinke/amber9/src/leap'
Compiling basic programs
cd src/Wc; make
make[2]: Entering directory `/home/jfinke/amber9/src/leap/src/Wc'
Makefile:10: warning: overriding commands for target `.c.o'
../../../config.h:86: warning: ignoring old commands for target `.c.o'
icc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -o MapAg.o MapAg.c
icc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -o WcActCB.o WcActCB.c
WcActCB.c(22): catastrophic error: could not open source file "X11/IntrinsicP.h" #include <X11/IntrinsicP.h>

compilation aborted for WcActCB.c (code 4)
make[2]: *** [WcActCB.o] Error 4
make[2]: Leaving directory `/home/jfinke/amber9/src/leap/src/Wc'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/home/jfinke/amber9/src/leap'
make: *** [serial] Error 2

attached mail follows:

> I am presently trying to install AMBER 9 on an SGI Altix 450 cluster but am having difficulty. Do you have a good recommedation for a compiler which works well with this system.

The Intel compilers, obviously. It would be extremely strange if you
had an Altix system with no access to the Intel compilers.

> It appears from the installation instructions that a g95 compiler is
> recommended.

Huh... which instructions are you reading?

You should try this first:

./configure nopar sgi_altix

This sets you up for a serial version on the Altix, then when you're
OK that it works,

./configure mpi sgi_altix

sets up the parallel version.

> I have also tried an ifort compiler which works for the smaller programs but not sander (an error appears regarding a program "icc" which I am not familiar with and was not installed with our cluster).

icc is the Intel C compiler. If it isn't installed, your Altix
installation is seriously FUBAR.

Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
+358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
< URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
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Received on Wed Mar 12 2008 - 06:07:32 PDT
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