AMBER Archive (2008)

Subject: RE: AMBER: Problems compiling leap on Altix Cluster

From: Ross Walker (
Date: Mon Nov 03 2008 - 18:06:07 CST

Hi John


There is no way on this earth that this can work if you just copied the
libraries over from a different version of Linux - they are very very
tightly coupled into the exact version of X that you have installed. On your
Altix I am guessing that you have SuSe installed (just a guess you should
double check) in which case you would need to do something along the lines


1) Carefully remove the stuff you copied over.

2) Install the correct X11 development library RPM - this is probably
something along the lines of:



This is what I got from an Altix running: Welcome to SUSE Linux Enterprise
Server 10 SP1 (ia64) - Kernel \r (\l).


On your system this maybe a different version. You can take a look at what
xorg version is installed with:


rpm -qa | grep xorg-x11


e.g. xorg-x11-6.9.0-50.52


In which case you need to get this version of xorg-x11-devel and then
install it - with say rpm -ivh xorg-x11-devel.XXXXX


Note Suse has some kind of package management system called yast. I have
never used it but it may be able to automatically download and install this
for you.


If your OS is something other than Suse then the above procedure may be


Alternatively if you just want to do away with xleap and install everything
else then just do:


edit $AMBERHOME/src/Makefile


Comment out line 32: cd leap; make install

uncomment line 38: cd leap/src/leap; make -f Makefile.tleap install


Then build things again.


Good luck,




From: [] On Behalf Of
John Finke
Sent: Monday, November 03, 2008 3:43 PM
Subject: Re: AMBER: Problems compiling leap on Altix Cluster



Somehow I missed your message on Friday. I apologize for sending the email

Anyway, I copied the libraries from my RedHat 9.0 computer to the Altix.
(You were right, these were missing).

The compilation gets past the xTank.c step but then runs into a series of
errors involving programs which begin with "xa":

(there may be more, the list was longer than my screen would scroll up to).

An example of the errors is shown below for the xaTools.c and
xaAngleParmTable.c programs. The errors of the other xa programs are very
similar (undefined references).

xaTools.o: In function `xtcpXATDefineBitmap':
xaTools.c:(.text+0x212): undefined reference to `XtVaSetValues'
xaTools.o: In function `XATPrintStringToWidget':
xaTools.c:(.text+0x732): undefined reference to `XtCallActionProc'
xaTools.c:(.text+0x742): undefined reference to `XtDisplay'
xaTools.c:(.text+0x752): undefined reference to `XFlush'
xaTools.o: In function `zXATAddBitmap??unw':
xaTools.c:(.text+0x842): undefined reference to `XCreateBitmapFromData'
xaTools.o: In function `XATInitializeTools':
xaTools.c:(.text+0xad2): undefined reference to `WcRegisterCallback'

xaAngleParmTable.o: In function `zcPXAVPTVerifyRow??unw':
xaAngleParmTable.c:(.text+0xae2): undefined reference to `XawTableSetLabel'
xaAngleParmTable.c:(.text+0xb02): undefined reference to `XawTableSetLabel'
xaAngleParmTable.o: In function `XAVPTPopupTable':
xaAngleParmTable.c:(.text+0x1e52): undefined reference to

What are your suggestions to deal with this.

Thanks again,

John Finke


On 11/3/08, Ross Walker <> wrote:

Hi John,


Did you install the X11/xorg development libraries like I suggested in my
message on Friday?


All the best



From: [] On Behalf Of
John Finke
Sent: Monday, November 03, 2008 12:52 PM
Subject: AMBER: Problems compiling leap on Altix Cluster


I have been having trouble compiling the leap programs on an Altix SGI
machine. This problem does not occur on computers running RedHat 9.0.

To simplify the compiling situation, I have been attempting to compile the
leap program individually using the ifort compiler (I get the same error
when I compile the entire AMBER 9 program as well).

"cd $AMBERHOME/src/leap/src/leap"

"make clean"

The program compiles up to a point but the following error occurs and the
compilation exits before completion.

icc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2
-o xTank.o xTank.c
xTank.c(62): catastrophic error: could not open source file
"X11/IntrinsicP.h" #include <X11/IntrinsicP.h>

compilation aborted for xTank.c (code 4)
make: *** [xTank.o] Error 4

As a quick fix, I commented out line 62 of xTank.c like so:

/* #include <X11/IntrinsicP.h> */

but then the error above still occurs but with the next X11 directory file
from line 63, <X11/StringDefs.h> instead of <X11/IntrinsicP.h>.

With the xTank.c program, files in the X11 directory are a problem for some
reason. They do not appear to be a problem with other subroutines in the
leap directory which also reference files in the X11 directory. So it is a
bit of a mystery to me.

Any suggestions on how to locate this IntrinsicP.h file, the X11 directory
to which the code is refering to, or comment out the lines which are killing
the compilation (and still allows the program to run)?


John Finke


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