Re: AMBER: Problems compiling leap on Altix Cluster

From: John Finke <>
Date: Mon, 3 Nov 2008 18:43:09 -0500


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
> Ross
> *From:* [] *On
> Behalf Of *John Finke
> *Sent:* Monday, November 03, 2008 12:52 PM
> *To:*
> *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"
> "make"
> 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)?
> Thanks,
> John Finke

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Received on Fri Dec 05 2008 - 10:34:51 PST
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