Greeting colleagues,
I would like to convey my thanks to everyone who responded to my
inquiry. The number of responses was small enough for me to paste them
below. I employed the first listed solution and it worked fine. If
anyone needs the files mentioned please don't hesitate to contact me.
Below is a description of the errors I received during expinstall and
> during my attempts to compile an au program.
>
> After doing an expinstall, with inclusion of the 'recompile all user
> AU programs', I get an error on a screen with a heading of 'CPR'
>
> The screen has a line that says ' edau command standard error
> listing'. This is followed by a long list of lines with the word
> 'exiting' on them.
>
> When I try to run 'iexpno' in the command window I get the following
> error:
>
> CANNOT FIND
>
> "opt/xwinnmr/prog/au/bin/iexpno"
>
> when I look in the bin folder all I see are two files named iexpno.c
> and iexpno.E
Bruker asked me to send the output shown below, and from this they
determined that the compiler was not working.
# export XWINNMRHOME=/opt/xwinnmr
# ./makeau -verbose iexpno
makeau ($Revision: 1.84.2.13 $)
OperatingSystem=LINUX
Red Hat Enterprise Linux AS release 3 (Taroon Update 4)
Search: 1=,2=,3=Enterprise,4=
Red Hat Enterprise Linux AS release 3 (Taroon Update 4)
=> using NATIVE compiler!
Setup for native compiler
CC=gcc
LD=c++
Installed RPM packages:
glibc-2.3.2-95.30
glibc-devel-2.3.2-95.30
package kernel-headers is not installed
package kernel-source is not installed
used kernel release: 2.4.21-27.0.2.EL
Known paths:
.
/opt/xwinnmr/prog/bin/scripts
/usr/kerberos/sbin
/usr/kerberos/bin
/usr/local/sbin
/usr/local/bin
/sbin
/bin
/usr/sbin
/usr/bin
/usr/X11R6/bin
/root/bin
Current environment:
HOME=/root
SSH_CLIENT=128.148.119.87 3533 22
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
SSH_CONNECTION=128.148.119.87 3533 128.148.119.30 22
_RLD_ARGS=-ignore_unresolved
LESSOPEN=|/usr/bin/lesspipe.sh %s
MAIL=/var/spool/mail/root
PWD=/opt/xwinnmr/exp/stan/nmr/au
LANG=en_US.UTF-8
USER=root
XWINNMRHOME=/opt/xwinnmr
G_BROKEN_FILENAMES=1
LOGNAME=root
USERNAME=root
SHLVL=1
HOSTNAME=oksana
OLDPWD=/
INPUTRC=/etc/inputrc
_=./makeau
PATH=.:/opt/xwinnmr/prog/bin/scripts:/usr/kerberos/sbin:/usr/kerberos/bi
n:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R
6/bin:/root/bin
LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:bd=40;33;01:cd
=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=01;32:*.cmd=01;32:*.exe=01;32
:*.com=01;32:*.btm=01;32:*.bat=01;32:*.sh=01;32:*.csh=01;32:*.tar=01;31:
*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.
Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tz=01;31:*.rpm=01;31:*.cpio=
01;31:*.jpg=01;35:*.gif=01;35:*.bmp=01;35:*.xbm=01;35:*.xpm=01;35:*.png=
01;35:*.tif=01;35:
BASH_ENV=/root/.bashrc
SHELL=/bin/bash
HISTSIZE=1000
TERM=vt100
SSH_TTY=/dev/pts/0
LibraryExtension: .so
LibraryPath: shlib
ObjectExtension: .o
BinaryExtension:
BinaryExtension:
Check for /opt/xwinnmr/exp/stan/nmr/au/paravision_3.6.pl
Check for /opt/xwinnmr/exp/stan/nmr/au/user_3.6.pl
submacro(/opt/xwinnmr/prog/include/inc
/opt/xwinnmr/exp/stan/nmr/au/src/iexpno
/opt/xwinnmr/prog/au/bin/iexpno.E)
No INC_FLAGS found: using default library list
Used libraries:
auliba
aulibp
chparmod
plotpar
rwmeta
meta
sxutil
libhpcu
libBpsu
ConvSf
libSwish
libVtu
lib_sbsb
lib_tty
librrs
liblrs
Bis
convpw
editpar
libacq
util
rwmeta
aulibp
uni
par
libPath
libcb
libUtil
libCUtil
libShapeIO
libFunc
libJCamp
libCt
Included Libraries
auliba.so
aulibp.so
chparmod.so
plotpar.so
rwmeta.so
meta.so
sxutil.so
libhpcu.so
libBpsu.so
ConvSf.so
libSwish.so
libVtu.so
lib_sbsb.so
lib_tty.so
librrs.so
liblrs.so
Bis.so
convpw.so
editpar.so
libacq.so
util.so
rwmeta.so
aulibp.so
uni.so
par.so
libPath.so
libcb.so
libUtil.so
libCUtil.so
libShapeIO.so
libFunc.so
libJCamp.so
libCt.so
Combine /opt/xwinnmr/exp/stan/nmr/au/vorspann
/opt/xwinnmr/prog/au/bin/iexpno.E > /opt/xwinnmr/prog/au/bin/iexpno.c
Include Option: -I/opt/xwinnmr/prog/include
chdir /opt/xwinnmr/prog/au/bin
Opersys=LINUX
gcc -c -DLINUX_INTEL -D_REENTRANT -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -g -w -v -I/opt/xwinnmr/prog/include
-DOLD_META_MEMORY /opt/xwinnmr/prog/au/bin/iexpno.c
exit=16777215 sig=127 dump=128
exiting
========================================================================
==================================================
This is the solution I employed. Special thanks to Harold Toms.
Yes, the C compiler is clearly not working, that is the stage of
compilation that is failing. I actually use 3.5.6 with Linux (I fixed
the various things that don't work myself before they brought out 3.6)
and one difference is that au programs are compiled with the gcc
compiler that Bruker provide rather than the native Linux gcc. I note
that the new (3.6) version of the script "makeau" uses the native Linux
compiler which for some reason isn't working. I don't know for sure if
this will work, but if Bruker still include their own gcc with the
XWINNMR release it may be worth trying to use this instead. To do this
you need to:
1) Check that Bruker have included a gcc program (it will be in the
directory $XWINNMRHOME/gnu/bin where you should find the gcc program.
2) If it is there replace the current "makeau" script with the 3.5.6 one
(I've attached a copy). Do this by *copying the old one first* (so you
can easily restore it) then replacing it with the attached one (the
script is in $XWINNMRHOME/exp/stan/nmr/au).
3) You need to similarly replace two *system* files with ones that I
have attached. These are /usr/lib/crt1.o and /usr/lib/libc_nonshared.a.
Again *copy the originals first before installing the replacements*.
If Bruker don't include gcc etc... any more you can get them from the
3.5.6 CD if you have it or *possibly* I can send it to you - it may be
too large for e-mail. It may also be that the makeau script includes an
option for using the Bruker version of gcc (which would be simpler than
steps 1-3), I haven't got the script to look at but you should be able
to get options by typing "./makeau -help" (you need to be in the
directory $XWINNMRHOME/exp/stan/nmr/au to do this).
========================================================================
==================================================
We are running XWinNMR 3.5 on a Red Hat 9 machine. We introduced two
changes to get the compiling to work. Although this doesn't completely
match your system it might be worth to try.
1) New makeau script
http://chemnmr.colorado.edu/ammrl/archives/May-2003/26.html
2) Link to shared library
(also
http://chemnmr.colorado.edu/ammrl/archives/May-2003/26.html)
cd /opt/xwinnmr/prog/shlib
ln -s libstdc++-libc6.1-2.so.3 libstdc++.so
2) Environment variable set
setenv LD_ASSUME_KERNEL 2.4.1 (preferable in .cshrc)
========================================================================
==================================================
~~~~~~~~~~~~~~~~~~~~~~~~
Russ Hopson, Ph.D.
NMR Facility Supervisor
Brown University
Department of Chemistry, Box H
Providence, RI 02912
(o) - 401-863-3069
(b) - 401-235-8306
Received on Fri Mar 18 2005 - 10:46:59 MST