Search found 29 matches

by bangdt
Thu Jan 16, 2020 7:56 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.08

Dear Kate It is long time no see, I hope you are doing well. thank you so much for help us go through this forum smoothly. several months ago I have install pyroms 2 and successfully made boundary and initial file. Today after install pyroms 3 (python 3) it return an error. when I run this code impo...
by bangdt
Sat Jun 29, 2019 1:17 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

What you want is to call do_file for each file in the list. Did it print the list of files to operate on? Is it what you expected? Then you can comment out the chunk with processes = 4 to the end. Add a loop going through the list of files, calling do_file(file, src_grd, dst_grd), something like: f...
by bangdt
Thu Jun 27, 2019 10:51 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

Maybe this is biting you: memorylocked 16384 kbytes Dear Kate by running this code (pr2) root@C2:~# ulimit -l 16384 (pr2) root@C2:~# ulimit -l unlimited (pr2) root@C2:~# ulimit -l unlimited then my system has (pr2) root@C2:~# ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimi...
by bangdt
Wed Jun 26, 2019 1:47 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

You can read up on multiprocessing online. Something wasn't right about your last attempt. I would check your system limits. With a bash shell: My information (pr2) bangdt@C2:~$ ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks...
by bangdt
Tue Jun 25, 2019 12:11 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

Can you try on a system with more memory? I restart and try to run it and the err stills remain. My system is 8gb of ram with nearly 6gb free. May be problem is related to system open mpi libraries can not linked to anaconda packages? I have succeced running ROMS test cases with mpi run. I try to r...
by bangdt
Mon Jun 24, 2019 7:46 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

kate wrote:Does it object to processes = 1 the same way as processes = 4, or was there a different error? What if you don't let it kill the job?
I have same err for 4 and 1 processes. If i dont kill it then the script hang like picture above with no err message and activity.
by bangdt
Mon Jun 24, 2019 6:21 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

Maybe you should try a pool size of 1, not running in parallel. I'm not familiar with that exact display, but the swap seems high, like it doesn't all fit in memory and none of them are making any progress. Dear Kate Thanks for help. I put some flag into the code then so I have error with p = Pool(...
by bangdt
Mon Jun 24, 2019 1:21 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

The limits on these two types of jobs are different, and you might have run into some system limits on cputime, etc. Do you have a sys admin to talk to about where and how to run jobs? . Dear Kate Thank you for help. I am trying to run all in my laptop before asking admin about my cputime. I run th...
by bangdt
Sun Jun 23, 2019 5:45 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

year = int(sys.argv[1]) Did you give it a year as a command-line argument? It is expecting one. There's also a commented out line: #lst_year = sys.argv[1:] that can be enabled, allowing you to give it a list of years. Or you can edit the script to provide the year(s) internally. For the other, I th...
by bangdt
Sun Jun 23, 2019 3:34 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

My latest version of that troublesome line is: h[j,i] = depth_bnds[int(bottom[j,i])+1] Sometimes it pays to "git pull". Step 5 happens with this script: #!/bin/ksh print -n "Enter year to process: "; read year; print "" leap=`echo $(($year % 4))` if [ $leap == 0 ] ; then nday=366 else nday=365 fi #...
by bangdt
Sat Jun 22, 2019 8:55 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

Sometimes Python evolves so that something that used to run no longer runs. Sometimes when that happens I can figure out how to change it and get it pushed to github. You need to update your code through either "git pull" or just editing it in place. Dear Kate Thank you so much, I do git pull and u...
by bangdt
Sat Jun 22, 2019 3:56 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

My latest version of that troublesome line is: h[j,i] = depth_bnds[int(bottom[j,i])+1] Sometimes it pays to "git pull". Dear Kate by looking in get_nc_Grid_HYCOM.py I have for i in range(1,len(depth)): depth_bnds[i] = 0.5 * (depth[i-1] + depth[i]) depth_bnds[-1] = 5750 It suggested that after that,...
by bangdt
Sat Jun 22, 2019 2:26 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

Are you sure you are downloading on the GLBa0.08 HYCOM grid? They have moved that to the "inactive" status. It was on a tripole grid and needed lat,lon to be functions if both i and j. The newer HYCOM products are on a simpler grid, where lat is a function of j only and lon is a function of i only....
by bangdt
Wed Jun 19, 2019 2:42 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

No, I don't think you have a version problem, unless it's a HYCOM version problem. lon_t = lon[1:-1,1:-1] Longitude is often a 1-D array, not a 2-D array. What do you have? Dear Kate I am sorry, I still do not understand my problem. I would like to make IC BC from this data https://ncss.hycom.org/t...
by bangdt
Tue Jun 18, 2019 6:05 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

Looks like it should be 'depth', not 'z'. Dear Kate you are right I changed it to depth and pass, and have this error after that >>> srcgrd = pyroms_toolbox.Grid_HYCOM.get_nc_Grid_HYCOM('/work/apps/anaconda3/envs/pr2/lib/python2.7/site-packages/pyroms_toolbox/works/East-Sea_HYCOM/Hycomdata/19062012...
by bangdt
Tue Jun 18, 2019 4:48 am
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Re: Create boundary and initial file from seagrid and GLBa0.

. First you run make_remap_weights_file, then make_ic_file/make_bdry_file. A more equatorial example is in Palau_HYCOM. Dear Kate I download Hycom data with empty z (to import all z to the netcdf file) then try to run make_remap_weights_file and got problem with this -------------------------------...
by bangdt
Mon Jun 17, 2019 5:08 pm
Forum: ROMS Tools and Techniques
Topic: Create boundary and initial file from seagrid and GLBa0.08
Replies: 32
Views: 1611

Create boundary and initial file from seagrid and GLBa0.08

Hi everyone, please help me to create boundary and initial file from seagrid and GLBa0.08 - Hycom data. I created seagrid nc file for my domain and have Hycom data. I also install pyroms_toolbox. My problem is I have no idea about how to make boundary and initial file. Could anybody help me a exampl...
by bangdt
Sun Jun 16, 2019 2:14 am
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 1058

Re: PYROMS error

The only use I know of for lpsolve is to smooth the bathymetry. I usually use pyroms for other tasks, not grid generation. What do you need pyroms to do for you? Dear Kate Thank you so much for your very quick and useful instructions. I am going to make boundary and initial file for r4dvar case tes...
by bangdt
Sat Jun 15, 2019 4:39 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 1058

Re: PYROMS error

Spectral has a capital "S". See for example this Stackoverflow thread . I don't know how you ended up with a lower case spectral. As for the other, my solution is that I don't use lpsolve. I think I once copied the thing to my current directory and that worked. Dear Kate Thank you for correct me ab...
by bangdt
Sat Jun 15, 2019 9:07 am
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 1058

Re: PYROMS error

This troublesome bit: Alternatively, you need to somehow provide makefile2 with the path to 'netcdf.inc', the Fortran include file for netCDF. You can change: LIBDIR = $(shell $(NC_CONFIG) --prefix)/lib INCDIR = $(shell $(NC_CONFIG) --prefix)/include to something like: LIBDIR = /usr/local/netcdf/li...
by bangdt
Fri Jun 14, 2019 3:15 am
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 1058

Re: PYROMS error

No, don't go backwards! We always had problems with python finding those libraries, so going backwards is not the answer. Stick with Python 3 and read the README where I tell you what I have to do for python to find the libraries - I just have copies in three different places, with hopes that at le...
by bangdt
Thu Jun 13, 2019 3:50 pm
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 1058

Re: PYROMS error

Type "git branch" to see which branch you have. The "python3" branch is the current default, so that is probably what you have already. As for those libraries, you need to make sure your LD_LIBRARY_PATH environment variable includes the directory they live in. Dear Kate Thank you so much for your r...
by bangdt
Thu Jun 13, 2019 3:32 am
Forum: ROMS Tools and Techniques
Topic: PYROMS error
Replies: 12
Views: 1058

Re: PYROMS error

The "master" branch of pyroms should work with Python 2.7. The code diffs for that line are: - print " Flinders Peak = %3i\xF8%3i\' %6.3f\", " % ( deg, minn, sec ), + print(" Flinders Peak = %3i\xF8%3i\' %6.3f\", " % ( deg, minn, sec ), end=' ') I have the new branch working in Python version 3.6.2...
by bangdt
Fri May 24, 2019 4:31 pm
Forum: ROMS Installation
Topic: ARPACK lib does not have `dsteqr_' `dpotri_' `dpotrf_'
Replies: 3
Views: 378

Re: ARPACK lib does not have `dsteqr_' `dpotri_' `dpotrf_'

Problem solved.
But I feel a little bit bored in lonely. :?
by bangdt
Fri May 24, 2019 9:14 am
Forum: ROMS Installation
Topic: ARPACK lib does not have `dsteqr_' `dpotri_' `dpotrf_'
Replies: 3
Views: 378

Re: ARPACK lib does not have `dsteqr_' `dpotri_' `dpotrf_'

I have solved the problem by linking the right mpich version for ROMS to use. With the same config for ARmake I built lparpack and larpack. From this I have make RomsM and run with ./build_roms.bash -j 4 roms_wc13.in the model run for about 2hours and hang with 100% cpu usage but no change in bash w...
by bangdt
Thu May 23, 2019 6:30 am
Forum: ROMS Installation
Topic: Help me please in runing build bash for shoreface test
Replies: 0
Views: 246

Help me please in runing build bash for shoreface test

when runing shoreface test I have these error =============================================== Found Error: ** Line: 4867 Source: ROMS/Modules/mod_netcdf.F, netcdf_get_fvar NETCDF_GET_TIME_0D - error while reading variable: wave_time in input file: Data/swan_shoreface_angle_forc.nc call from: ROMS/Ut...
by bangdt
Wed May 22, 2019 5:56 pm
Forum: ROMS Installation
Topic: ARPACK lib does not have `dsteqr_' `dpotri_' `dpotrf_'
Replies: 3
Views: 378

ARPACK lib does not have `dsteqr_' `dpotri_' `dpotrf_'

I recently compiled ARPACK with ARmake.mpif90-Linux file and set FFLAGS = -u -Bstatic -c -frepack-arrays -O3 -ffast-math -O3 -w -fno-strict-overflow The version used is come with trunk/LIB folder which is described that support for compile and run ROMS. recently known problem with ARPACK and `dsteqr...
by bangdt
Tue May 21, 2019 7:41 pm
Forum: ROMS Information
Topic: compile problem in R4DVAR
Replies: 5
Views: 2496

Re: compile problem in R4DVAR

Dear Sir Arango! When I tried to copile the ARPACK, because of my system I should choose the file ARmake.mpif90-Linux, but options of the file such as FC = mpif90 FFLAGS = -u -Bstatic -fastsse -Mipa=fast # Set the parallel fortran compiler PFC = mpif90 PFFLAGS = -u -Bstatic -fastsse -Mipa=fast Did n...