Dear Shaoqing,
Your problem is with the specification of ifort_ia64. Your machine is not an
Itanium IA64 chip. The Core 2 Duo's are x86_64 chips.
Hence you need to use.
./configure -static ifort_x86_64
then type which ifort and make sure it points to:
/opt/intel/fce/9.1.045/bin/ifort
The fce is the important bit. If it is /fc/ then it is the wrong one, that
is the x86 version while you want the 'fce' x86_64 version.
E.g.:
Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version 9.1
Build 20060925 Package ID: l_fc_c_9.1.039
Copyright (C) 1985-2006 Intel Corporation. All rights reserved.
Note the EM64T-based applications!!!
Since you were using a i386 compiler on an x86_64 machine with a config.h
file for a 64 bit Itanium it is no wonder you have been having problems.
All the best
Ross
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Shaoqing.Zhang.mail.uh.edu
Sent: Monday, January 08, 2007 09:06
To: amber.scripps.edu
Subject: Re: AMBER: question about the testing of AMBER9
Thank you very much for your continuing help. Here are my answers to the
questions.
1)What type of machine are you running this on?
$ more /proc/cpuinfo
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 15
model name : Intel(R) Core(TM)2 CPU 6300 . 1.86GHz
stepping : 6
cpu MHz : 1862.051
cache size : 2048 KB
physical id : 0
siblings : 2
core id : 0
cpu cores : 2
fpu : yes
fpu_exception : yes
cpuid level : 10
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall lm
constant_ts
c pni monitor ds_cpl vmx est tm2 cx16 xtpr lahf_lm
bogomips : 3726.85
clflush size : 64
cache_alignment : 64
address sizes : 36 bits physical, 48 bits virtual
power management:
processor : 1
vendor_id : GenuineIntel
cpu family : 6
model : 15
model name : Intel(R) Core(TM)2 CPU 6300 . 1.86GHz
stepping : 6
cpu MHz : 1862.051
cache size : 2048 KB
physical id : 0
siblings : 2
core id : 1
cpu cores : 2
fpu : yes
fpu_exception : yes
cpuid level : 10
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall lm
constant_ts
c pni monitor ds_cpl vmx est tm2 cx16 xtpr lahf_lm
bogomips : 3724.11
clflush size : 64
cache_alignment : 64
address sizes : 36 bits physical, 48 bits virtual
power management:
2)What distro are you running
2.6.18-1.2239.fc5 #1 SMP Fri Nov 10 12:51:06 EST 2006 x86_64 x86_64 x86_64
GNU/Linux
3) What version of ifort and icc are you using?
Intel-icc91045 - 9.1.045-1.i386 - Intel(R) C++ Compiler for 32-bit
applications, version 9.1 (9.1.045)
Intel-ifort91040 - 9.1.040-1.i386 - Intel(R) C++ Compiler for 32-bit
applications, version 9.1 (9.1.040)
4) What does "rpm -qi libXt" return?
$ rpm -qi libXt
Name : libXt Relocations: (not relocatable)
Version : 1.0.0 Vendor: Red Hat, Inc.
Release : 2.2 Build Date: Sat 11 Feb 2006
06:54:06 PM CST
Install Date: Thu 30 Nov 2006 03:22:03 PM CST Build Host:
hs20-bc1-1.build.redhat.com
Group : System Environment/Libraries Source RPM:
libXt-1.0.0-2.2.src.rpm
Size : 409337 License: MIT/X11
Signature : DSA/SHA1, Mon 06 Mar 2006 05:50:46 PM CST, Key ID
b44269d04f2a6fd2
Packager : Red Hat, Inc. <http://bugzilla.redhat.com/bugzilla>
URL : http://www.x.org
Summary : X.Org X11 libXt runtime library
Description :
X.Org X11 libXt runtime library
Name : libXt Relocations: (not relocatable)
Version : 1.0.0 Vendor: Red Hat, Inc.
Release : 2.2 Build Date: Sat 11 Feb 2006
06:59:25 PM CST
Install Date: Thu 30 Nov 2006 03:22:18 PM CST Build Host:
ls20-bc1-13.build.redhat.com
Group : System Environment/Libraries Source RPM:
libXt-1.0.0-2.2.src.rpm
Size : 368729 License: MIT/X11
Signature : DSA/SHA1, Mon 06 Mar 2006 05:50:44 PM CST, Key ID
b44269d04f2a6fd2
Packager : Red Hat, Inc. <http://bugzilla.redhat.com/bugzilla>
URL : http://www.x.org
Summary : X.Org X11 libXt runtime library
Description :
X.Org X11 libXt runtime library
5)What parameters did you pass to $AMBERHOME/src/configure to build the
config.h ?
I find sander can be executable, but there is trouble with leap. I already
added -L/usr/lib -L/usr/lib64 to config.h. Here I have several configure
options using different compilor names.
----------------------------------------------------------------------------
------
1. $ ./configure ifort_ia64 (This is what I first used)
Warning: the AMBERHOME environment variable is not defined !
It usually should be set to the path of Amber's top level directory.
Caution: Setting AMBERHOME to /home/amber9/amber9 !
Setting up Amber configuration file for architecture: ifort_ia64
Using parallel communications library: none
The MKL_HOME environment variable is not defined.
The configuration file, config.h, was successfully created.
IN THE LEAP DIRECTORY, I "make" and get this error message:
icc -o xaLeap basics.o sysdepend.o ...(omitted) xaHBondParmTable.o
../Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a ../Xmu/libXmu.a
-L/usr/X11R6/lib64 -L/usr/X11R6/lib -L/usr/lib -L/usr/lib64 -lXt -lXext -lSM
-lICE -lX11 -lm -lpthread
ld: skipping incompatible /usr/lib64/libXt.so when searching for -lXt
ld: skipping incompatible /usr/lib64/libXt.so when searching for -lXt
ld: cannot find -lXt
make[1]: *** [xaLeap] Error 1
make[1]: Leaving directory `/home/amber9/amber9/src/leap/src/leap'
make: *** [install] Error 2
----------------------------------------------------------------------------
--
2. $ ./configure ifort_ia32
Warning: the AMBERHOME environment variable is not defined !
It usually should be set to the path of Amber's top level directory.
Caution: Setting AMBERHOME to /home/amber9/amber9 !
Setting up Amber configuration file for architecture: ifort_ia32
Using parallel communications library: none
The MKL_HOME environment variable is not defined.
The MKL is recommended for optimal performance.
The configuration file, config.h, was successfully created.
IN THE LEAP DIRECTORY, I "make" and get a different error message:
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -o ScrolledTable.o ScrolledTable.c
ScrolledTable.c:1167: error: conflicting types for
‘XawScrolledTableSetLocation’
ScrolledTable.h:99: error: previous declaration of
‘XawScrolledTableSetLocation’ was here
make[1]: *** [ScrolledTable.o] Error 1
make[1]: Leaving directory `/home/amber9/amber9/src/leap/src/Xraw'
make: *** [install] Error 2
-------------------------------------------------------------
3. $ ./configure ifort_x86_64
The same output as with ifort_ia32.
The same error message with ifort_ia32.
-----------------------------------------------------------
4. $ ./configure gfortran
The same output with ifort_ia64.
The same error message with ifort_ia32.
Looking forward to your reply. Thank you for your efforts.
Shaoqing
----- Original Message -----
From: Mark Williamson <Mark.Williamson.imperial.ac.uk>
Date: Monday, January 8, 2007 3:40 am
Subject: Re: AMBER: question about the testing of AMBER9
To: amber.scripps.edu
> Shaoqing.Zhang.mail.uh.edu wrote:
> > Thank you very much for your reply. I tried what you
> suggested; however,
> > it doesn't work. Do you think there is something to do with
> the "icc"
> > compiler?
> >
>
> 1) What type of machine are you running this on?
>
> 2) What distro are you running (I've been assuming FC5 upto this
> point
> in the thread)
>
> 3) What version of ifort and icc are you using?
>
> 4) What does "rpm -qi libXt" return?
>
> 5) What parameters did you pass to $AMBERHOME/src/configure to
> build the
> config.h ?
>
> regards,
>
> Mark
>
> -----------------------------------------------------------------
> ------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
----- Original Message -----
From: Mark Williamson <Mark.Williamson.imperial.ac.uk>
Date: Monday, January 8, 2007 3:40 am
Subject: Re: AMBER: question about the testing of AMBER9
To: amber.scripps.edu
> Shaoqing.Zhang.mail.uh.edu wrote:
> > Thank you very much for your reply. I tried what you
> suggested; however,
> > it doesn't work. Do you think there is something to do with
> the "icc"
> > compiler?
> >
>
> 1) What type of machine are you running this on?
>
> 2) What distro are you running (I've been assuming FC5 upto this
> point
> in the thread)
>
> 3) What version of ifort and icc are you using?
>
> 4) What does "rpm -qi libXt" return?
>
> 5) What parameters did you pass to $AMBERHOME/src/configure to
> build the
> config.h ?
>
> regards,
>
> Mark
>
> -----------------------------------------------------------------
> ------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
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Received on Wed Jan 10 2007 - 06:07:29 PST
