[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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