[ncl-install] ncl rhel6 binary install - error while testing

[Mary Haley]

I think the issue may be with your libXext set of files. The error is saying that they are "incompatible".

Did you upgrade your operating system lately? If so, you may need to update the X11 libraries as well.

Also, which NCL binary file did you download, and what version of gfortran/gcc do you have?

The error is complaining about a libXext that's associated with gcc 4.4.6. If you have a newer version of gcc (higher than 4.5), then this may also be an issue.

Please make sure you have the correct X11 libraries installed on your system and give the ncargex command a try again. You may need reinstall libX11rather than just updating it.

--Mary

On Jul 5, 2013, at 8:35 AM, Doraiswamy, Prakash wrote:

> Hi Mary,
> 
> Thanks very much for the quick response.  I would like to transition to ncl at some point, but I have ncarg programs from a while back and would like to write similar programs until I get fully familiar with ncl.  Thanks for your suggestions.  Here is the complete output without any changes, when I execute the command “ncargex cpex08 –clean”:
> 
> NCAR Graphics Fortran  Example <cpex08>
> 
>  Copying cpex08.f
> 
>  Copying cpexcc.f
> 
> Compiling and linking...
> gfortran -fPIC -fno-second-underscore -O -o cpex08 cpexcc.f cpex08.f -L/usr/local/ncl-6.1.2/lib -L/usr/X11R6/lib64 -lncarg -lncarg_gks -lncarg_c -lX11 -lXext -lcairo -lfontconfig -lpixman-1 -lfreetype -lexpat -lpng -lz -lpthread -lbz2 -lXrender
> /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../libXext.so when searching for -lXext
> /usr/bin/ld: skipping incompatible /usr/lib/libXext.so when searching for -lXext
> /usr/bin/ld: cannot find -lXext
> collect2: ld returned 1 exit status
> 
> The compile and link failed.
> 
> 
> 
> Next, I modified the syslibdir in $NCARG_ROOT/bin/ncargf77.  It originally had “-L/usr/X11R6/lib64”.  That directory is non-existent.  I changed it to “-L/usr/lib64” and executed the command again, but still got the same error (except for the change in the path):
> 
> NCAR Graphics Fortran  Example <cpex08>
> 
>  Copying cpex08.f
> 
>  Copying cpexcc.f
> 
> Compiling and linking...
> gfortran -fPIC -fno-second-underscore -O -o cpex08 cpexcc.f cpex08.f -L/usr/local/ncl-6.1.2/lib -L/usr/lib64 -lncarg -lncarg_gks -lncarg_c -lX11 -lXext -lcairo -lfontconfig -lpixman-1 -lfreetype -lexpat -lpng -lz -lpthread -lbz2 -lXrender
> /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../libXext.so when searching for -lXext
> /usr/bin/ld: skipping incompatible /usr/lib/libXext.so when searching for -lXext
> /usr/bin/ld: cannot find -lXext
> collect2: ld returned 1 exit status
> 
> The compile and link failed.
> 
> I tried “yum update libXext” and “yum reinstall libXext”, but to no avail – I am still getting the same message. 
> 
> Thanks,
> Prakash
> 
> ************************************************
> Prakash Doraiswamy, Ph.D.
> Research Environmental Scientist-2
> Environmental & Industrial Sciences Division
> RTI International
> 
> 3040 East Cornwallis Road
> Post Office Box 12194
> Research Triangle Park, NC 27709-2194
> 
> Ph: 919-990-8648
> e-mail: pdoraiswamy at rti.org
> ************************************************
> 
> From: Mary Haley [mailto:haley at ucar.edu] 
> Sent: Thursday, July 04, 2013 7:45 PM
> To: Doraiswamy, Prakash
> Cc: ncl-install at ucar.edu
> Subject: Re: [ncl-install] ncl rhel6 binary install - error while testing
> 
> Hi,
> 
> If you plan to just use NCL, then don't worry about the fact that "ncargex cpex08" failed.  You only need this to work if you plan to write NCAR Graphics C or Fortran programs and compile them.
> 
> If you really want to get this to work, then it looks like either your compiler is finding the wrong Xext library on your system, or else you have an incorrect installation of it.
> 
> You didn't include the full output from "ncargex cpex08", so I'm not sure what "-L" paths it is using, but my guess it that it needs "-L/usr/lib64" on the compile line.
> 
> You might try editing $NCARG_ROOT/bin/ncargf77 
> 
> and modify the line that looks something like this:
> 
> set syslibdir = "-L/usr/lib"
> 
> to have something like this:
> 
> set syslibdir = "-L/usr/lib64"
> 
> 
> The "ncargf77" command gets called by the "ncargex" command, so once you make this change and save the file, try running the "ncargex cpex08 -clean" command again.
> 
> --Mary
> 
> On Jul 3, 2013, at 4:31 PM, "Doraiswamy, Prakash" <pdoraiswamy at rti.org> wrote:
> 
> 
> Hi,
> 
> I downloaded the following binary version of the NCL/NCARG package:
> 
> ncl_ncarg-6.1.2.Linux_RHEL6.2_x86_64_nodap_gcc472.tar.gz
> 
> and placed the extracted folders in /usr/local and updated NCARG_ROOT path in my cshrc file.
> 
> When I tested the installation: “ng4ex gsun01n” worked fine, but the ncarg test “ncargex cpex08” failed.  Here is the error message I am getting:
> 
> /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../libXext.so when searching for –lXext
> /usr/bin/ld: skipping incompatible /usr/lib/libXext.so when searching for –lXext
> /usr/bin/ld: cannot find –lXext
> Collect2: ld returned 1 exit status
> The compile and link failed.
> 
> I see the following files installed when I do ls *Xext* in /usr/lib and /usr/lib64:
> 
> /usr/lib/libXext.so   (symbolic link to so.6.4.0)
> /usr/lib/libXext.so.6  (symbolic link)
> /usr/lib/libXext.so.6.4.0
> 
> /usr/lib64/libXext.so.6
> /usr/lib64/libXext.so.6.4.0
> 
> I have RHEL6 on my cluster. gcc –v  returns “gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC)”
> 
> Can you please guide as to where the problem might be?  I even tried with the binary ending in gcc446.tar.gz, but still got the same message.  Thanks for your help.
> 
> Thanks,
> Prakash
> 
> 
> ************************************************
> Prakash Doraiswamy, Ph.D.
> Research Environmental Scientist-2
> Environmental & Industrial Sciences Division
> RTI International
> 
> 3040 East Cornwallis Road
> Post Office Box 12194
> Research Triangle Park, NC 27709-2194
> 
> Ph: 919-990-8648
> e-mail: pdoraiswamy at rti.org
> ************************************************
> 
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