AMBER Archive (2007)

Subject: Re: AMBER: question about the testing of AMBER9

From: Shaoqing.Zhang_at_mail.uh.edu
Date: Mon Jan 08 2007 - 11:06:18 CST


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_at_imperial.ac.uk>
Date: Monday, January 8, 2007 3:40 am
Subject: Re: AMBER: question about the testing of AMBER9
To: amber_at_scripps.edu

> Shaoqing.Zhang_at_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_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

----- Original Message -----
From: Mark Williamson <Mark.Williamson_at_imperial.ac.uk>
Date: Monday, January 8, 2007 3:40 am
Subject: Re: AMBER: question about the testing of AMBER9
To: amber_at_scripps.edu

> Shaoqing.Zhang_at_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_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

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