<div dir="ltr"><div class="gmail_default" style="font-size:small">Hi Elena,</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">It sounds to me like your environment is not quite right.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">As an example, when I run a batch job on our supers and I want to use the GNU version of NCL, I have to make sure I'm in the GNU compiler environment before I run NCL:</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">module load gnu</div><div class="gmail_default" style="font-size:small">module load ncl</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Maybe you need to do something similar?</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">In general, you shouldn't have to mess with environment variables like LD_LIBRARY_PATH. </div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">--Mary</div><div class="gmail_default" style="font-size:small"><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Mon, Jan 7, 2019 at 2:23 AM Elena Kropac via ncl-install <<a href="mailto:ncl-install@ucar.edu">ncl-install@ucar.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div style="font-family:Verdana;font-size:12px"><div>Dear NCL support,</div>
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<div>I have an issue submitting an NCL script to slurm with sbatch. I am working in the field of Climate Modeling at a university in Germany and they provide a computing cluster which is a Linux RedHat 4.8.5-36 with gcc 4.8.5 (see below for further system information). I need to run an NCL script which uses the ESMF_RegridWeightGen function and takes too long to be run from the comand line (it runs without errors but is killed automatically after some 8 hrs because of computational expense). Therefore, I want to submit the script to slurm using sbatch. However, when I do so, I get the error <span style="font-family:"Courier New",Courier,monospace">"ncl: error while loading shared ibraries: libgomp.so.1: cannot open shared object file: No such file or directory"</span>.</div>
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<div>I have searched for the "missing" library using <span style="font-family:"Courier New",Courier,monospace">yum provides "*/libgomp.so.1"</span> and found <span style="font-family:"Courier New",Courier,monospace">libgomp.so.1</span> (<span style="font-family:"Courier New",Courier,monospace">libgomp-4.8.5-36.el7.x86_64</span>) in <span style="font-family:"Courier New",Courier,monospace">/usr/lib64/</span>. I added this path to my <span style="font-family:"Courier New",Courier,monospace">LD_LIBRARY_PATH</span> which did, however, not have any effect - I keep getting the same error.</div>
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<div>I currently have a pre-compiled version of NCL 6.4.0 installed (ncl_ncarg-6.4.0-RHEL6.4_64bit_nodap_gnu447.tar.gz), but I have already tried other binaries and versions. When I use the ncl_ncarg-6.5.0-CentOS7.5_64bit_nodap_gnu485.tar.gz one, which should match my compiler version, I get the same error, but refering to the <span style="font-family:"Courier New",Courier,monospace">libgfortran.so.3</span> library.</div>
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<div>I guess I might have an older version of the gfortran compiler on my system than what NCL was compiled with, but I do not quite know what the problem is, especially as the script is running in comand line without throwing me an error message. The error only appears when I try to submit the script to slurm. Do you have an idea what the problem could be and how to solve it? As I am working on a externally administrated cluster, I cannot simply install any files with <span style="font-family:"Courier New",Courier,monospace">sudo</span>. But if that is necessary to get the script running, I can ask the system administrator.</div>
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<div>Here is some further information about my system:</div>
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<pre>which ncl -> /home/hpc/gwgk/gwgi006h/LIBRARIES/ncl-6.4.0/bin/ncl
ncl -V -> 6.4.0
env | grep NCARG -> NCARG_ROOT=/home/hpc/gwgk/gwgi006h/LIBRARIES/ncl-6.4.0
NCARG_LIB=/home/hpc/gwgk/gwgi006h/LIBRARIES/ncl-6.4.0/lib
which gcc -> /usr/bin/gcc
which gfortran -> /usr/bin/gfortran
gfortran --version -> GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36)
gcc --version -> gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36)</pre>
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Best regards,</div>
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<div>Elena Kropac</div></div></div>
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