[ncl-talk] problem with ncl_filedump *.nc ?

Sam McClatchie smcclatchie at fishocean.info
Wed Sep 19 00:53:10 MDT 2018


Hi Rick

Thanks for looking into this. I do have the csh shell installed, but 
ncl_filedump gives the same error on my Ubuntu system:

smcc at jaguar:/data/dynamic_data/scratch$ which csh
/bin/csh
smcc at jaguar:/data/dynamic_data/scratch$ /bin/csh
% ncl_filedump sst.nc
Segmentation fault
% /bin/bash
smcc at jaguar:/data/dynamic_data/scratch$

I did not install NCL 6.5.0 with conda. I just used the pre-compiled 
binary, as described on this page: 
<http://www.ncl.ucar.edu/Download/install.shtml>. I did not remove ncl 
6.4.0 first, but the new install goes into its own directory.

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.

And yes, the basic functionality that you have requested me to test 
below works. For example the following code works fine.
The graphic produced is here 
<https://my.pcloud.com/publink/show?code=XZvWI17Z2aF9F5VtdsXoRsHmt74BQQTkec4y> 

The data are here: 
<https://my.pcloud.com/publink/show?code=XZ8sI17ZM2y7639vxwFin6gmJR0ET0pwFKH7>

And the code is here:

;=============================
; read in data
in                       = 
addfile("/data/dynamic_data/datasets/currents_Copernicus_CMEMS_model_satellite/dataset-uv-rep-monthly_1536962814624.nc","r")
time                     = in->time
depth                    = in->depth
lat                      = in->latitude
lon                      = in->longitude
uo                       = in->uo
vo                       = in->vo
  ; print(vo)

wks                      = 
gsn_open_wks("png","../figures/monthly_mean_total_surface_and_15m_velocities" 
)

; plot options
res                      = True
; set coastline resolution
res at mpDataBaseVersion    = "MediumRes"

res at gsnAddCyclic         = False
; labelling/ label positions
res at tiMainString         = "Monthly mean surface (15m) velocities"
res at gsnRightStringOrthogonalPosF = -1.2
res at gsnRightStringParallelPosF = 1.1

; subset the region
res at mpMinLatF            = 25   ; range to zoom in on
res at mpMaxLatF            = 45.
res at mpMinLonF            = -130
res at mpMaxLonF            = -110.
; contours
res at cnLevelSelectionMode = "ManualLevels"
res at cnMinLevelValF       = -0.5
res at cnMaxLevelValF       = 0.5
res at cnLevelSpacingF    = 0.05 ; contour spacing

res at mpGridAndLimbOn      = True              ; turn on lat/lon lines
res at mpPerimOn            = False             ; turn off box around plot
res at mpGridLatSpacingF    = 5.               ; spacing for lat lines
res at mpGridLonSpacingF    = 5.               ; spacing for lon lines
res at mpFillOn             = False

res at cnFillOn             = True              ; color plot desired
res at cnFillPalette        = "cmocean_balance"     ; set color map
res at cnLineLabelsOn       = False             ; turn off contour lines
res at txFontHeightF        = 0.015

; res at vpXF               = 0.1                 ; make plot bigger
; res at vpYF               = 0.9
; res at vpWidthF           = 0.8
; res at vpHeightF          = 0.8

res at lbLabelFontHeightF   = 0.015           ; label bar font height

plot_currents            = gsn_csm_contour_map(wks,uo(200,0,:,:),res)
; =================

Best fishes
Sam

On 19/09/18 14:24, Rick Brownrigg wrote:
> Hi Sam and Dylan,
>
> 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 :-(
>
> 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"?
>
> 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):
>
> $ ncl
> ncl 0> f = addfile("....your file...", "r")
> ncl 1> print(f)
>
> If either of you could//would, can you verify that at least this basic 
> functionality works?
>
> I wish I had a better answer... :-/
>
> Rick
>
>
> On Mon, Sep 17, 2018 at 9:54 PM, Rick Brownrigg <brownrig at ucar.edu 
> <mailto:brownrig at ucar.edu>> wrote:
>
>     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:
>       - emerged in 6.5.0
>       - both are c-shell drivers ultimately calling NCL
>       - all known incidents occur on Ubuntu systems
>
>     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.
>
>     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, :-/
>
>
>     ---------- Forwarded message ----------
>     From: *Sam McClatchie* <smcclatchie at fishocean.info
>     <mailto:smcclatchie at fishocean.info>>
>     Date: Mon, Sep 17, 2018 at 1:42 PM
>     Subject: Re: [ncl-talk] problem with ncl_filedump *.nc ?
>     To: Rick Brownrigg <brownrig at ucar.edu <mailto:brownrig at ucar.edu>>
>
>
>     Hello Rick
>
>     Thanks for looking into this. I am using Ubuntu 18.04. Here is the
>     output that you requested:
>
>     smcc at jaguar:/data/dynamic_data/scratch$ ldd `which ncl`
>         linux-vdso.so.1 (0x00007ffe281a0000)
>         libssl.so.1.1 => /usr/lib/x86_64-linux-gnu/libssl.so.1.1
>     (0x00007f2824005000)
>         libcrypto.so.1.1 => /usr/lib/x86_64-linux-gnu/libcrypto.so.1.1
>     (0x00007f2823b8d000)
>         libXrender.so.1 => /usr/lib/x86_64-linux-gnu/libXrender.so.1
>     (0x00007f2823983000)
>         libfontconfig.so.1 =>
>     /usr/lib/x86_64-linux-gnu/libfontconfig.so.1 (0x00007f282373e000)
>         libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0
>     (0x00007f282352e000)
>         libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6
>     (0x00007f28231f6000)
>         libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6
>     (0x00007f2822fe4000)
>         libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3
>     (0x00007f2822cb3000)
>         libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f2822915000)
>         libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2
>     (0x00007f2822711000)
>         libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
>     (0x00007f2822383000)
>         libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1
>     (0x00007f2822153000)
>         libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
>     (0x00007f2821f3b000)
>         libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
>     (0x00007f2821d1c000)
>         libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f282192b000)
>         /lib64/ld-linux-x86-64.so.2 (0x00007f28278cb000)
>         libfreetype.so.6 => /usr/lib/x86_64-linux-gnu/libfreetype.so.6
>     (0x00007f2821677000)
>         libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1
>     (0x00007f2821445000)
>         libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1
>     (0x00007f282121d000)
>         libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0
>     (0x00007f2820fdd000)
>         libpng16.so.16 => /usr/lib/x86_64-linux-gnu/libpng16.so.16
>     (0x00007f2820dab000)
>         libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f2820b8e000)
>         libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6
>     (0x00007f282098a000)
>         libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6
>     (0x00007f2820784000)
>         libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0
>     (0x00007f282056f000)
>         librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1
>     (0x00007f2820367000)
>
>     smcc at jaguar:/data/dynamic_data/scratch$ uname -a
>     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
>
>     smcc at jaguar:/data/dynamic_data/scratch$ gcc -v
>     Using built-in specs.
>     COLLECT_GCC=gcc
>     COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
>     OFFLOAD_TARGET_NAMES=nvptx-none
>     OFFLOAD_TARGET_DEFAULT=1
>     Target: x86_64-linux-gnu
>     Configured with: ../src/configure -v --with-pkgversion='Ubuntu
>     7.3.0-16ubuntu3'
>     --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs
>     --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
>     Thread model: posix
>     gcc version 7.3.0 (Ubuntu 7.3.0-16ubuntu3)
>     smcc at jaguar:/data/dynamic_data/scratch$
>
>     Best fishes
>     Sam
>
>     On 18/09/18 03:32, Rick Brownrigg wrote:
>>     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.
>>
>>     I wondering if I could get someone who is experiencing this issue
>>     to run:
>>
>>     ldd `which ncl`
>>     uname -a
>>     gcc -v
>>
>>     and send the output directly to me?
>>
>>     Rick
>
>     -- 
>     Sam McClatchie (fisheries oceanographer)
>     & Elena Turin (accounting & auditing)
>     FishOcean Enterprises
>     38 Upland Rd, Huia, Auckland 0604, New Zealand
>     <https://maps.google.com/?q=38+Upland+Rd,+Huia,+Auckland+0604,+New+Zealand&entry=gmail&source=g>
>     cell: 027 752 8495
>     Internet <http://www.fishocean.info>
>
>
>     "The time has come", the tui said,
>     "to talk of many things:
>     Of songs - and ferns - and flowering flax,
>     of Pukekos and dreams ..."
>
>     (not Lewis Carroll)
>
>

-- 
email signature Sam McClatchie (fisheries oceanographer)
& Elena Turin (accounting & auditing)
FishOcean Enterprises
38 Upland Rd, Huia, Auckland 0604, New Zealand
cell: 027 752 8495
Internet <http://www.fishocean.info>


"The time has come", the tui said,
"to talk of many things:
Of songs - and ferns - and flowering flax,
of Pukekos and dreams ..."

(not Lewis Carroll)
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