<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>Rick,<br><br></div>Thanks for trying to get to the bottom of this. For a bit more info, I installed from the pre-compiled binaries first and had the same problem, and then tried out the conda install where the problem persisted. I also had to install csh myself. Running those commands do indeed work, so I made a workaround that you or others may find useful.<br><br></div>In a file called "ncl_filedump.ncl", I have written the line<font face="monospace,monospace"> - </font>print(addfile(filePath,"r"))<br></div><div>Then, in a file called "ncl_filedump.csh", I have written the line - ncl filePath=\"$1\" ncl_filedump.ncl<br></div><div>And in my "~/.bashrc" file, I have added the line - alias ncl_filedump="csh /path/to/ncl_filedump.csh"</div><div><br></div><div>You'd have to replace "/path/to/ncl_filedump.csh" with where ever you've
placed the file, and this relies on "ncl_filedump.csh" and
"ncl_filedump.ncl" to be in the same directory. This uses C-shell to pass the variable "filePath" to the NCL script, and to run it, after you've sourced "~/.bashrc", you'd type "ncl_filedump /some/directory/<a href="http://file.nc">file.nc</a>", and it will print out the file information. I'm sure this is missing some of the functionality that the original ncl_filedump had, but it's good for now!<br><br></div><div>Thanks again for your help! Have a great day,<br></div><div>Dylan<br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Sep 19, 2018 at 2:53 AM Sam McClatchie <<a href="mailto:smcclatchie@fishocean.info">smcclatchie@fishocean.info</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Hi Rick<br>
<br>
Thanks for looking into this. I do have the csh shell installed, but
ncl_filedump gives the same error on my Ubuntu system:<br>
<br>
smcc@jaguar:/data/dynamic_data/scratch$ which csh<br>
/bin/csh<br>
smcc@jaguar:/data/dynamic_data/scratch$ /bin/csh<br>
% ncl_filedump <a href="http://sst.nc" target="_blank">sst.nc</a> <br>
Segmentation fault<br>
% /bin/bash<br>
smcc@jaguar:/data/dynamic_data/scratch$ <br>
<br>
I did not install NCL 6.5.0 with conda. I just used the pre-compiled
binary, as described on this page:
<a class="m_8549213092752364917moz-txt-link-rfc2396E" href="http://www.ncl.ucar.edu/Download/install.shtml" target="_blank"><http://www.ncl.ucar.edu/Download/install.shtml></a>. I did not
remove ncl 6.4.0 first, but the new install goes into its own
directory.<br>
<br>
It's beginning to sound to me like there may be a minor difference
between the conda install and the pre-compiled binary install on
Ubuntu that somehow affects ncl_filedump. <br>
<br>
And yes, the basic functionality that you have requested me to test
below works. For example the following code works fine.<br>
The graphic produced is here
<a class="m_8549213092752364917moz-txt-link-rfc2396E" href="https://my.pcloud.com/publink/show?code=XZvWI17Z2aF9F5VtdsXoRsHmt74BQQTkec4y" target="_blank"><https://my.pcloud.com/publink/show?code=XZvWI17Z2aF9F5VtdsXoRsHmt74BQQTkec4y></a>
<br>
The data are here:
<a class="m_8549213092752364917moz-txt-link-rfc2396E" href="https://my.pcloud.com/publink/show?code=XZ8sI17ZM2y7639vxwFin6gmJR0ET0pwFKH7" target="_blank"><https://my.pcloud.com/publink/show?code=XZ8sI17ZM2y7639vxwFin6gmJR0ET0pwFKH7></a><br>
<br>
And the code is here:<br>
<br>
;=============================<br>
; read in data<br>
in =
addfile("/data/dynamic_data/datasets/currents_Copernicus_CMEMS_model_satellite/<a href="http://dataset-uv-rep-monthly_1536962814624.nc" target="_blank">dataset-uv-rep-monthly_1536962814624.nc</a>","r")<br>
time = in->time<br>
depth = in->depth<br>
lat = in->latitude<br>
lon = in->longitude<br>
uo = in->uo<br>
vo = in->vo<br>
; print(vo) <br>
<br>
wks =
gsn_open_wks("png","../figures/monthly_mean_total_surface_and_15m_velocities"
)<br>
<br>
; plot options<br>
res = True<br>
; set coastline resolution<br>
res@mpDataBaseVersion = "MediumRes"<br>
<br>
res@gsnAddCyclic = False<br>
; labelling/ label positions<br>
res@tiMainString = "Monthly mean surface (15m) velocities"<br>
res@gsnRightStringOrthogonalPosF = -1.2<br>
res@gsnRightStringParallelPosF = 1.1<br>
<br>
; subset the region<br>
res@mpMinLatF = 25 ; range to zoom in on<br>
res@mpMaxLatF = 45.<br>
res@mpMinLonF = -130<br>
res@mpMaxLonF = -110.<br>
; contours<br>
res@cnLevelSelectionMode = "ManualLevels"<br>
res@cnMinLevelValF = -0.5<br>
res@cnMaxLevelValF = 0.5<br>
res@cnLevelSpacingF = 0.05 ; contour spacing<br>
<br>
res@mpGridAndLimbOn = True ; turn on lat/lon lines<br>
res@mpPerimOn = False ; turn off box around
plot<br>
res@mpGridLatSpacingF = 5. ; spacing for lat lines<br>
res@mpGridLonSpacingF = 5. ; spacing for lon lines<br>
res@mpFillOn = False<br>
<br>
res@cnFillOn = True ; color plot desired<br>
res@cnFillPalette = "cmocean_balance" ; set color map<br>
res@cnLineLabelsOn = False ; turn off contour
lines<br>
res@txFontHeightF = 0.015<br>
<br>
; res@vpXF = 0.1 ; make plot bigger<br>
; res@vpYF = 0.9<br>
; res@vpWidthF = 0.8<br>
; res@vpHeightF = 0.8<br>
<br>
res@lbLabelFontHeightF = 0.015 ; label bar font height<br>
<br>
plot_currents =
gsn_csm_contour_map(wks,uo(200,0,:,:),res)<br>
; =================<br>
<br>
Best fishes<br>
Sam<br>
<br>
<div class="m_8549213092752364917moz-cite-prefix">On 19/09/18 14:24, Rick Brownrigg
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hi Sam and Dylan,</div>
<div><br>
</div>
<div>I certainly appreciate both of you providing diagnostics in
trying to troubleshoot this matter. It pains me to say that:
i) you even have to experience this disruption, and ii) I can
not replicate (and thus troubleshoot) the problem in any
fashion :-( <br>
</div>
<div><br>
</div>
<div>I could not glean any insight from the traces. A
commonality seems to be Ubuntu, so I stood up a fresh Ubuntu
18.02 distro (on a virtual machine), and did a conda install
of ncl into a fresh environment, and things work as expected.
Of note - in the minimalist installation of Ubuntu 18.02, I
did have to do an "apt-get" to install tcsh/csh -- do either
of you recall this being an issue for you, and how did you
acquire your "C-shell"?</div>
<div><br>
</div>
<div>So, I don't get it -- ncl_filedump is nothing more than a
C-shell script that sets up a bunch of stuff and then calls
NCL to do little more than (if you were to do this from the
command-line):</div>
<div><br>
</div>
<div>$ ncl</div>
<div>ncl 0> f = addfile("....your file...", "r")</div>
<div>ncl 1> print(f)</div>
<div><br>
</div>
<div>If either of you could//would, can you verify that at least
this basic functionality works?</div>
<div><br>
</div>
<div>I wish I had a better answer... :-/</div>
<div><br>
</div>
<div>Rick</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Sep 17, 2018 at 9:54 PM, Rick
Brownrigg <span dir="ltr"><<a href="mailto:brownrig@ucar.edu" target="_blank">brownrig@ucar.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Long story short -- Kevin and I have been talking
about this issue with ncl_filedump, and another one he
pointed out involving ng4ex. The commonalities are:</div>
<div> - emerged in 6.5.0</div>
<div> - both are c-shell drivers ultimately calling NCL</div>
<div> - all known incidents occur on Ubuntu systems</div>
<div><br>
</div>
<div>I engaged one of the users to provide me shell-traces
and system-traces, but that was not revealing. He tells
me that if he simply starts NCL and opens one of the
problematic files with addfile(), everything is OK. <br>
</div>
<div><br>
</div>
<div>I can't replicate the problems anywhere on systems I
have access to, and am afraid we are going to have to
stand up an Ubuntu syetem (VM) somewhere to try and
replicate the issue, :-/ <br>
</div>
<div>
<div class="m_8549213092752364917h5">
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<div class="gmail_quote">---------- Forwarded
message ----------<br>
From: <b class="gmail_sendername">Sam
McClatchie</b> <span dir="ltr"><<a href="mailto:smcclatchie@fishocean.info" target="_blank">smcclatchie@fishocean.info</a>></span><br>
Date: Mon, Sep 17, 2018 at 1:42 PM<br>
Subject: Re: [ncl-talk] problem with
ncl_filedump *.nc ?<br>
To: Rick Brownrigg <<a href="mailto:brownrig@ucar.edu" target="_blank">brownrig@ucar.edu</a>><br>
<br>
<br>
<div text="#000000" bgcolor="#FFFFFF"> Hello
Rick<br>
<br>
Thanks for looking into this. I am using
Ubuntu 18.04. Here is the output that you
requested:<br>
<br>
smcc@jaguar:/data/dynamic_data/scratch$
ldd `which ncl`<br>
linux-vdso.so.1 (0x00007ffe281a0000)<br>
libssl.so.1.1 =>
/usr/lib/x86_64-linux-gnu/libssl.so.1.1
(0x00007f2824005000)<br>
libcrypto.so.1.1 =>
/usr/lib/x86_64-linux-gnu/libcrypto.so.1.1
(0x00007f2823b8d000)<br>
libXrender.so.1 =>
/usr/lib/x86_64-linux-gnu/libXrender.so.1
(0x00007f2823983000)<br>
libfontconfig.so.1 =>
/usr/lib/x86_64-linux-gnu/libfontconfig.so.1
(0x00007f282373e000)<br>
libbz2.so.1.0 =>
/lib/x86_64-linux-gnu/libbz2.so.1.0
(0x00007f282352e000)<br>
libX11.so.6 =>
/usr/lib/x86_64-linux-gnu/libX11.so.6
(0x00007f28231f6000)<br>
libXext.so.6 =>
/usr/lib/x86_64-linux-gnu/libXext.so.6
(0x00007f2822fe4000)<br>
libgfortran.so.3 =>
/usr/lib/x86_64-linux-gnu/libgfortran.so.3
(0x00007f2822cb3000)<br>
libm.so.6 =>
/lib/x86_64-linux-gnu/libm.so.6
(0x00007f2822915000)<br>
libdl.so.2 =>
/lib/x86_64-linux-gnu/libdl.so.2
(0x00007f2822711000)<br>
libstdc++.so.6 =>
/usr/lib/x86_64-linux-gnu/libstdc++.so.6
(0x00007f2822383000)<br>
libgomp.so.1 =>
/usr/lib/x86_64-linux-gnu/libgomp.so.1
(0x00007f2822153000)<br>
libgcc_s.so.1 =>
/lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00007f2821f3b000)<br>
libpthread.so.0 =>
/lib/x86_64-linux-gnu/libpthread.so.0
(0x00007f2821d1c000)<br>
libc.so.6 =>
/lib/x86_64-linux-gnu/libc.so.6
(0x00007f282192b000)<br>
/lib64/ld-linux-x86-64.so.2
(0x00007f28278cb000)<br>
libfreetype.so.6 =>
/usr/lib/x86_64-linux-gnu/libfreetype.so.6
(0x00007f2821677000)<br>
libexpat.so.1 =>
/lib/x86_64-linux-gnu/libexpat.so.1
(0x00007f2821445000)<br>
libxcb.so.1 =>
/usr/lib/x86_64-linux-gnu/libxcb.so.1
(0x00007f282121d000)<br>
libquadmath.so.0 =>
/usr/lib/x86_64-linux-gnu/libquadmath.so.0
(0x00007f2820fdd000)<br>
libpng16.so.16 =>
/usr/lib/x86_64-linux-gnu/libpng16.so.16
(0x00007f2820dab000)<br>
libz.so.1 =>
/lib/x86_64-linux-gnu/libz.so.1
(0x00007f2820b8e000)<br>
libXau.so.6 =>
/usr/lib/x86_64-linux-gnu/libXau.so.6
(0x00007f282098a000)<br>
libXdmcp.so.6 =>
/usr/lib/x86_64-linux-gnu/libXdmcp.so.6
(0x00007f2820784000)<br>
libbsd.so.0 =>
/lib/x86_64-linux-gnu/libbsd.so.0
(0x00007f282056f000)<br>
librt.so.1 =>
/lib/x86_64-linux-gnu/librt.so.1
(0x00007f2820367000)<br>
<br>
smcc@jaguar:/data/dynamic_data/scratch$
uname -a<br>
Linux jaguar 4.15.0-34-generic #37-Ubuntu SMP
Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64
x86_64 GNU/Linux<br>
<br>
smcc@jaguar:/data/dynamic_data/scratch$
gcc -v<span><br>
Using built-in specs.<br>
COLLECT_GCC=gcc<br>
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper<br>
OFFLOAD_TARGET_NAMES=nvptx-none<br>
OFFLOAD_TARGET_DEFAULT=1<br>
Target: x86_64-linux-gnu<br>
Configured with: ../src/configure -v
--with-pkgversion='Ubuntu 7.3.0-16ubuntu3'
--with-bugurl=<a class="m_8549213092752364917m_-8203994636335106497m_7793217584817406634m_7105659064281507133moz-txt-link-freetext">file:///usr/share/doc/gcc-7/README.Bugs</a>
--enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++
--prefix=/usr --with-gcc-major-version-only
--with-as=/usr/bin/x86_64-linux-gnu-as
--with-ld=/usr/bin/x86_64-linux-gnu-ld
--program-suffix=-7
--program-prefix=x86_64-linux-gnu-
--enable-shared --enable-linker-build-id
--libexecdir=/usr/lib
--without-included-gettext
--enable-threads=posix --libdir=/usr/lib
--enable-nls --with-sysroot=/
--enable-clocale=gnu
--enable-libstdcxx-debug
--enable-libstdcxx-time=yes
--with-default-libstdcxx-abi=new
--enable-gnu-unique-object
--disable-vtable-verify --enable-libmpx
--enable-plugin --enable-default-pie
--with-system-zlib --with-target-system-zlib
--enable-objc-gc=auto --enable-multiarch
--disable-werror --with-arch-32=i686
--with-abi=m64
--with-multilib-list=m32,m64,mx32
--enable-multilib --with-tune=generic
--enable-offload-targets=nvptx-none
--without-cuda-driver
--enable-checking=release
--build=x86_64-linux-gnu
--host=x86_64-linux-gnu
--target=x86_64-linux-gnu<br>
Thread model: posix<br>
gcc version 7.3.0 (Ubuntu 7.3.0-16ubuntu3) <br>
</span> smcc@jaguar:/data/dynamic_data/scratch$
<br>
<br>
Best fishes<span class="m_8549213092752364917m_-8203994636335106497m_7793217584817406634HOEnZb"><font color="#888888"><br>
Sam</font></span><span><br>
<br>
<div class="m_8549213092752364917m_-8203994636335106497m_7793217584817406634m_7105659064281507133moz-cite-prefix">On
18/09/18 03:32, Rick Brownrigg wrote:<br>
</div>
<blockquote type="cite">
<div>This is odd -- I am able to dump all
of these files, using my development
version (which is still very 6.5.0-ish)
and a bonafide 6.5.0 as installed via
conda -- everything runs just fine.</div>
<div><br>
</div>
<div>I wondering if I could get someone
who is experiencing this issue to run:</div>
<div><br>
</div>
<div>ldd `which ncl`</div>
<div>uname -a</div>
<div>gcc -v</div>
<div><br>
</div>
<div>and send the output directly to me?<br>
</div>
<div><br>
</div>
<div>Rick</div>
</blockquote>
<br>
</span><span>
<div class="m_8549213092752364917m_-8203994636335106497m_7793217584817406634m_7105659064281507133moz-signature">--
<br>
Sam McClatchie (fisheries oceanographer)<br>
& Elena Turin (accounting &
auditing)<br>
FishOcean Enterprises<br>
<a href="https://maps.google.com/?q=38+Upland+Rd,+Huia,+Auckland+0604,+New+Zealand&entry=gmail&source=g" target="_blank">38
Upland Rd, Huia, Auckland 0604, New
Zealand</a><br>
cell: 027 752 8495<br>
<span style="text-decoration:underline"><a href="http://www.fishocean.info" target="_blank">Internet</a></span><br>
<img style="width:150px;height:149px" alt="" src="cid:part7.81BFC268.542F1F04@fishocean.info"><br>
<br>
"The time has come", the tui said,<br>
"to talk of many things:<br>
Of songs - and ferns - and flowering flax,<br>
of Pukekos and dreams ..."<br>
<br>
(not Lewis Carroll) </div>
</span></div>
</div>
<br>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
<div class="m_8549213092752364917moz-signature">-- <br>
Sam McClatchie (fisheries oceanographer)<br>
& Elena Turin (accounting & auditing)<br>
FishOcean Enterprises<br>
38 Upland Rd, Huia, Auckland 0604, New Zealand<br>
cell: 027 752 8495<br>
<span style="text-decoration:underline"><a href="http://www.fishocean.info" target="_blank">Internet</a></span><br>
<img style="width:150px;height:149px" alt="" src="cid:part7.81BFC268.542F1F04@fishocean.info"><br>
<br>
"The time has come", the tui said,<br>
"to talk of many things:<br>
Of songs - and ferns - and flowering flax,<br>
of Pukekos and dreams ..."<br>
<br>
(not Lewis Carroll)
</div>
</div>
</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span style="color:rgb(102,102,102)"><font size="2" face="arial, helvetica, sans-serif"><b>J. Dylan White</b></font></span></div><div><span style="color:rgb(102,102,102)">Ph.D. Student, Atmospheric Sciences<font size="2" face="arial, helvetica, sans-serif"><b><br></b></font></span></div><div><span style="color:rgb(102,102,102)">N.C. State University</span></div><div><span style="color:rgb(102,102,102)"><font size="2" face="arial, helvetica, sans-serif">B.S. Physics & B.S. Mathematics<br></font></span></div><div><span style="color:rgb(102,102,102)"><font size="2" face="arial, helvetica, sans-serif">Cell: 703.232.8920</font></span></div><div><br></div><div><font color="#888888"><br></font></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>