Ocean Modeling Discussion

robertson

The links in viewtopic.php?t=268 should now work. I converted them to mp4 files.

robertson

Hi, thank you for your reply. Here is my loaded module (module list): Currently Loaded Modules: 1) craype-x86-genoa 4) perftools-base/23.12.0 7) CmrsEnv/default 10) perlbrew/5.38.2 13) cray-dsmml/0.2.2 16) PrgEnv-intel/8.5.0 2) libfabric/1.20.1 5) xpmem/2.9.6-1.1_20240510205610__g087dc11fc19d 8 ...

robertson

After you have PrgEnv-intel/8.5.0 , cray-netcdf , and cray-hdf loaded, what does module list return? Also, what is the output of the ifort --version command? I would suggest you compile the code with USE_DEBUG=on in your build script so we can get a better sense of where in the code it is failing.

robertson

Most likely you checked out the code without the git-lfs filters enabled. In the instructions section for the roms_test repository we give a couple different options. The issue is that git itself won't download large files like NetCDF files, so git-lfs (Large File Support) is needed to download the ...

robertson

Try having your sysadmin install libopenmpi-dev. It looks like the mpif.h you're looking for is contained in that package. It seems that Ubuntu requires the -dev package in order to actually compile with openmpi.

robertson

What files are in your '/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/mpich' directory?

Also, depending on the OS (redhat style vs. debian/ubuntu style), enter one of the following commands and report back what is listed.

rpm -qa | grep mpi

or:

apt list --installed | grep mpi

robertson

Check that you have the latest non-beta Xcode and command line tools installed.

robertson

Are you certain that the 'mpirun' you used is at /home/jmette/openmpi/bin?

robertson

I just remembered that you are using cbuild_roms.sh and not build_roms.sh . I also checked the brew formula for netcdf and netcdf-fotran and neither is keg-only so there should be symlinks for libnetcdf.dylib and libnetcdff.dylib in ${HOMEBREW_PREFIX}/lib (probably /opt/homebrew/lib ) if libnetcdf ...

robertson

I use macports instead of homebrew. It appears from the output you shared above that homebrew puts the the netcdf-c libraries in a different directory than netcdf-fortran. There are several ways to fix this, the easiest is take the -L part of the output of ' nc-config --libs ' and add a LIBS =+ line ...

robertson

Setting netcdf lib and inc dirs as environment variables is really only for very old NetCDF versions where the fortran and c functions all reside in a single libnetcdf.a file and nf-config does not exits. What you want to do is set the environment variable NF_CONFIG to nf-config since that ...

robertson

I am unsure what version actually corrected this compiler bug but I'm happy to report that Intel OneAPI 2024.0 (i.e. 2021.11.1 for the classic compilers) fixes this problem.

robertson

Hmm, not sure if I understand. Which ROMS version on github, the 'develop' branch or the 'main' branch? Which revision should we use with the currently available tutorial? You should use the default develop branch on GitHub for pretty much everything. Think of develop as the latest svn revision and ...

robertson

There should be a variable name printed after the colon, i.e. "unable to define variable: ubar". Your error does not include a variable name. If you read further down in the log you will see: ERROR: Abnormal termination: NetCDF OUTPUT. REASON: NetCDF: Name contains illegal characters Looking at the ...

robertson

As of now, the only fix is to use 2023.0.0 or older. It is questionable whether Intel will fix this since they are phasing out the classic C/C++ (icc/icpc) and Fortran (ifort) compilers in favor of their newer LLVM based counterparts (icx, icpx, and ifx).

robertson

You might also consider updating your ROMS source code; the revision you are using is over 3.5 years old.

robertson

Yes, this is indeed a syntax error caused by a typo: S.checksum should be S%checksum.

Thank you for reporting this error. The correction has been made, please update your code.

robertson

Yes, this is indeed a syntax error caused by a typo: S.checksum should be S%checksum.

Thank you for reporting this error. The correction has been made, please update your code.

robertson

Several observations/questions: My first guess would be that you downloaded the code with a different computer than you are trying to build on. Some of your paths seem to be incorrect ( nf-config , netcdf.mod and mpif90 not found) The permissions inside the source code are wrong: ROMS/Bin/cpp_clean ...

robertson

I was able to reproduce your error by installing and using the same version of the Intel compiler ( 2023.2.0 released July 13, 2023). I tracked the issue in the TotalView debugger and appears to be a compiler bug. If you have access to an earlier version of the compiler I would try using that ...

robertson

What compiler and version are you using?

robertson

Do you have USE_MPI and USE_MPIF90 set in your build script? If so, I would guess that your system has Intel MPI installed and in your path and you didn't change which_MPI to be set to intel . To access the MPI enabled Intel Fortran compilers when you are using Intel's MPI implementation, you need ...

robertson

This would indicate that you checked out the ROMS source code on a Windows machine then tried to build it on a non-Windows system. The '^M' is how Windows (DOS actually) style line endings/carriage returns are interpreted by non-Windows systems.

robertson

If everything is consistent, the error would suggest that there is a typo somewhere that is making ROMS think it's supposed to be building something called '8'. Perhaps there's a path with a space in it or just an errant '8'?

robertson

You will need to build NetCDF4/HDF5 with the Intel compilers and update your build script (and probably my_build_paths.sh) to point to the correct location for the NetCDF built with Intel.

robertson

How and when did you download your ROMS source code? The bash build script has not been named build.bash for almost 4 years and is now called build_roms.sh . Are you perhaps trying to use an old build.bash with the new source code? If so, I would suggest starting anew with the build_roms.sh file ...

robertson

I believe the issue is that your roms_almirante.in file is out of date. Several new parameters were added since 3.8. In particular, you are missing INP_LIB and OUT_LIB . Compare your .in file with one of the roms_*.in files in the ROMS/External folder of your new source code and add any missing ...

robertson

Could you also attach your tides_date.f90 from your Build_romsG directory?

robertson

If you have access to ifort I would definitely recommend using that rather than gfortran.

robertson

In our experience "signed integer overflow" runtime error with gfortran is a non-fatal error and ROMS will continue to run. The real problem is likely the stack trace that comes next. My first guess would be that something is missing or mistyped in your .in and or varinfo.yaml file. If you are using ...

robertson

Is that the full output of the build attempt? What command and options are you using to build? Are there any other differences between the build in your home directory and dfs? For example, different modules loaded or a different compiler, etc. What does the command ' /usr/bin/cpp --version ' give ...

robertson

make sure that the mpirun you are using is from the same openmpi directory that you compiled with. For example, if you are compiling with /self/compiled/openpmi/bin/mpif90 make sure that the command which mpirun returns /self/compiled/opempi/bin/mpirun and not something like /usr/bin/mpirun If the ...

robertson

You need to actually "cd" into the run directory. You create it and copy files into it but you never actually change into RUN_DIR.

robertson

The homebrew installed NCL (NCAR Graphics) was built for x86-64 (presumably under the Rosetta 2) but you are attempting to build the package for arm64. I'm not familiar with homebrew but a quick google search suggests maybe trying to install ncl with:

Code: Select all

arch -arm64 brew install ncl

robertson

Check your .in file. ROMS is telling you that you don't have a consistent order of values for Lm (and probably others). In your case, since you have 4 grids (Ngrids = 4), there should be 4 values, separated by spaces that correspond to your 4 grids in order . The values should be Lm for grid 1, grid ...

robertson

Double check your main makefile and make sure there are no libNLM.a references in there and that all other recent changes are there as well. Somewhere there is a reference to libNLM.a. Maybe not all the Module.mk files were updated properly? Check ROMS/Nonlinear/Module.mk first.

robertson

You need remove "$(SCRATCH_DIR)/libNLM.a" from line 51 of your Linux-ifort.mk so it reads: LIBS := By setting LIBS to "$(SCRATCH_DIR)/libNLM.a" you are asking the make system to build that library. However, there is no longer a rule do so because ROMS now builds a single library instead of one for ...

robertson

Vname is referenced 4 times in that code block. Which line is 1895? Also, that code block occurs 3 times in mod_ncparam.f90; which CASE block is line 1895 under? You will need to scroll up about 15 lines to see what CASE block you are in.

robertson

The fix for this was released two days ago in revision 1119 (Ticket 913). Please update your ROMS code.

robertson

In your build script, uncomment the "export USE_NETCDF4=on" line. This only tells ROMS that your NetCDF library is version 4 so it can link properly, it will not result in NetCDF4/HDF5 format output files. Also, whenever you post in the ROMS forum about an error you are encountering, the MOST ...

robertson

The error implies that the netcdf module your are attempting you use was built with a newer version of ifort than you are currently attempting to use. Are you sure you have attached the build script you used? Your build script has USE_MPI and USE_MPIF90 commented out yet the model is trying to ...

robertson

Recompile your code in debug mode (un-comment the USE_DEBUG line in your build_roms.sh or build_roms.csh ), then run your model again with the resulting romsG (instead of romsM or romsS) executable. That will hopefully give you an idea where in the code the segfault is coming from to narrow down the ...

robertson

What compiler are you using? This error is almost certainly due to ROMS trying to take advantage of so called wrap-around addition for random number generation. Line 150 of your ran1.f90 is likely: ranv(1:n)=ieor(nran(1:n),ranv(1:n))+mran(1:n) Some compilers have decided to treat overflows as an ...

robertson

It appears from your output that you have not set USE_MY_LIBS to yes in your roms_build.sh . If you had, there would be a note about the full path to the my_build_paths.sh file being loaded. That is probably why you found it necessary to edit Darwin-gfortran.mk . I would suggest: undoing your edits ...

robertson

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robertson

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robertson

Your machine has 44 real cores with hyper-threading resulting in 88 CPUs being listed. Open MPI (and all other MPI implementations I have used) looks at your real cores only and that is the limit for mpirun. You can override this by issuing the --oversubscribe flag in your mpirun command but even ...

robertson

FORT was undefined, but FC was defined with intel... So, ROMS setup was defaulting to setting things up for PGI then actually doing the compilation with IFORT. Somehow wasn't an issue when setting up 3.9 (beyond strings of warnings). Fixed by simply adding FORT=intel. ROMS uses a combination of ...

robertson

I see some rather amazing technical issues with that build. First it appears that you somehow have a mix of pgf90 (PGI), ifort (Intel), and gfortran (GNU). The compiling flags (-fastsse -Mipa=fast -Kieee) in your build are for the PGI compilers, suggesting that you have either not set FORT or set it ...

robertson

We need to see the link line that produces that error so we can see if you have the all the includes and libraries that you need listed.

robertson

USE_PIO (and USE_SCORPIO ) are used only by the build script to add PIO (or SCORPIO) libraries and includes to the ROMS compilation configuration. They do not automatically define the PIO_LIB CPP option. The same is true of USE_NETCDF4 which does not instruct ROMS to output NetCDF4/HDF5 files. You ...

robertson

REC needs to start at 1 not 0

robertson

It may be because you have not listed a coastline file after the grid file. I believe the coastline file is required even if your plotted area does not have any land.

robertson

Is it possible that you are trying to run an OpenMP (shared memory) ROMS executable using an 'mpirun' command? You have -fopenmp in your list of flags but the multiple occurrences of: -------------------------------------------------------------------------------- Model Input Parameters: ROMS/TOMS ...

robertson

In order have any idea what is going on we would need to see the error after you fixed your tiling error.

robertson

During the upgrade to ubuntu 20.04 the GNU Compilier Suite was likely upgraded to version 9.3. Assuming you built NetCDF 4.7.4 yourself, your options are: build NetCDF again with the new compiler, downgrade the compiler, or install the libnetcdff-dev and netcdf-bin packages (this will also install a ...

robertson

If indeed this path is correct /home/bangdt/netcdf-3.6.1/lib then that is an incredibly old build of NetCDF (3.6.1 Released 02/26/2006). At any rate, either you didn't build the Fortran interface or you split the library and there is both a libnetcdf and libnetcdff in that lib directory. For the ...

robertson

My guess is that /Users/sean/bin doesn't exist. Error number 2 is "No such file or directory".

robertson

You appear to be using a combination of Homebrew and anaconda so perhaps that is contributing to your issues. That said, in older versions of ncl/ncarg there was a separate library ( libncarg_gks_cairo.a) that had several added dependencies ( -lcairo -lfontconfig -lpixman-1 -lfreetype etc.). Some ...

robertson

Using an NCL/NCARG built with the system's gnu (4.8.5) is very unlikely to work with a NetCDF/HDF5 and ROMS plotting package compiled with Intel compilers. You have 2 options, find or compile NCL/NCARG with the Intel compilers or find or compile NetCDF/HDF5 with the GNU 4.8.5 compilers.

robertson

Try installing cairo and freetype (probably called freetype2) libraries. If they are already installed, make sure they are the 64-bit versions and are in the library search path.

robertson

I also just noticed that your csecG executable seems to be link to libgfortran as well. Perhaps your version of NCAR Graphics was built with gfortran instead of the Intel compilers. What is your NCARG_ROOT environment variable set to?

robertson

It looks like the netcdf and HDF5 you are linking with were compiled with a much older (2016) Intel compiler than you are using to compile the plotting package (2020). Do you have access to the Intel 2016 compiler? If so, try compiling the plotting package with that version instead.

robertson

Is it possible that when the plotting package runs it's actually using a different NetCDF than you compiled with? If you are running Linux type: ldd /path/to/csecG with /path/to replaced by the correct path to csecG. Make sure that the libnetcdf listed by the ldd command is the one you compiled ...

robertson

You could try building the plotting package with PLT_DEBUG turned on. That might give you a better idea where the error is occurring. Building with debug will not replace your existing csec, etc. but will instead create a csecG, etc. in the MY_PROJECT_DIR, which is usually the directory you execute ...

robertson

The plotting package also has build scripts in src/Bin. However, the build scripts for the plotting packages have not been updated to use "my_build_paths" so the paths are set further down in the script. For the build_plt.bash script I believe you will need to edit lines 279 and 280. From your other ...

robertson

When you installed NetCDF, which packages did you choose? I believe if you choose "libnetcdf-fortran-devel" that should, as long as you allow the dependencies to install, get you everything you need as far as NetCDF is concerned. However, I have not tried this in many years so I could be missing ...

robertson

You need to completely remove the line:

Code: Select all

!Wind-Driven Upwelling/Downwelling over a Periodic Channel

The plotting package is expecting "nfields" to be line 6. There can't be any missing or commented lines until line 45 and the order matters.

robertson

As noted near the end of the topic you referenced, we recommend against compiling your own NetCDF when working in Cygwin. The Cygwin installer includes binary packages NetCDF and also includes OpenMPI if you would like to run the model in parallel.

robertson

I'm guessing you have a typo near the bottom:

cean_avg1_00001.nc

robertson

In the makefile inside the src directory replace: NEED_VERSION := 3.80 3.81 3.82 $(if $(filter $(MAKE_VERSION),$(NEED_VERSION)),, \ $(error This makefile requires one of GNU make version $(NEED_VERSION).)) with: ifneq (3.80,$(firstword $(sort $(MAKE_VERSION) 3.80))) $(error This makefile requires ...

robertson

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robertson

That is correct. I thought I had replaced all the occurrences of 'ocean*' with 'roms*' in the wiki but I clearly missed some. I corrected several more pages this morning but, out of curiosity, on which page did you find the reference to 'oceanS'?

robertson

I'm not sure where homebrew is getting their patches but they are missing some important things and are actually further from a usable product than the netcdf-fortran 4.5.3 release is. I believe home brew puts symlinks to all libraries in /usr/local/lib so, if you have the proper permissions, I ...

robertson

Maybe something was corrupted during transfer? What command(s) did you use to transfer to your own server? What operating system is "South Sea" and what operating system is your "own server"?

robertson

Your error is still in the linking. Those object files with no symbols are normal and most of them relate to the 4D-Var system which isn't used for the upwelling test case. From the paths you have shared, I'm assuming that you are using a Mac with Homebrew. What appears to be the issue is the 'nf ...

robertson

At the start of your output from the build script, which 'my_build_paths.sh' does it say it's loading and does it match the path to the one you have updated. From your latest post of the ROMS link line it looks like there aren't any NetCDF libraries linking at all now. What is returned when you type ...

robertson

Since you executed the build script as root, the Build_roms directory is owned by root so user javadbabagoli does not have permission to remove it. Manually remove (rm -rf Build_roms) the Build_roms directory as root. Then run the build script (as javadbabagoli) again. If you still get permission ...

robertson

That svn error should not stop compilation and the command that is failing is only used for informational purposes. Compiling (and running) ROMS as root is never a good idea. It's also quite likely that somewhere along the line you made a directory that is owned by root and that is probably what isn ...

robertson

It doesn't really agree with the error you're getting but are you absolutely sure you have write permissions to the directory you're writing the history file to?

robertson

In your build script enable "USE_NETCDF4". This will allow the build system to get the proper library locations and names to link your executable.

robertson

When I open your .in and .h files my editor says they are "dos" format. However, from your log output it does not look like you are running on a windows system. Did you, by chance, edit these files in Windows? If your system has 'dos2unix' run that on any files you edited in Windows. If not you can ...

robertson

Typically /bin/sh errors are due to the build script not being able to find an executable. Most often it is the compiler but can also be nf-config or others. My first guess would be the build script is unable to find your compiler. Check that whatever compiler you're asking it to find (and mpif90 if ...

robertson

you problem is: 12 levsfrc Deepest level to apply surface stress as a bodyforce. READ_PHYPAR - Invalid input parameter, levsfrc = 12 Out of range surface bodyforce level. Found Error: 05 Line: 191 Source: ROMS/Utility/inp_par.F Found Error: 05 Line: 115 Source: ROMS/Drivers/nl_ocean.h, ROMS ...

robertson

I would suggest trying Windows Subsystem for Linux (WSL) if that is an option for you. More information can be found here . We don't have a tutorial for that but, once you have your WSL setup, the procedure should be the same as regular Linux. The Cygwin tutorial in the wiki is very old and many ...

robertson

Perhaps Conda didn't put libX11 in a location the linker knows about. Find out where libX11 actually resides and make sure that path is in the LD_LIBRARY_PATH and LIBRARY_PATH environment variables.

robertson

You probably need to do: export MY_ROOT_PATH=/cygdrive/d/Agathe/Ecole/Modele3D/software/roms and: export MY_ROMS_SRC=${MY_ROOT_DIR}/Projects/trunk You should always avoid spaces in assignments when using bash. There should be no space before or after an equals sign during assignments

robertson

enter home directory 'cd ~' and enter commands in single command line vi .netrc machine www.myroms.org login rdfleay password -my password- protocol https terminal does some funky run.. I have adjusted the documentation to clarify but vi is a common text editor you could use to enter the next few ...

robertson

I have rearranged the documentation on the WikiROMS Git page so instructions for setting up a credential manager comes before instructions for downloading the code.

robertson

I have not confirmed this, but I believe that the "git checkout" and/or "git rev-parse" commands actually result in multiple git commands being executed and each git command is asking for your password. Set up a credential manager (explained further down on the ROMS Git wiki page) and try again ...

robertson

Try updating your varinfo.dat file.

robertson

Torque is likely the resource manager/job scheduler on the cluster you are using. Since it is a system specific library (and it's not listed in the ROMS link line you have provided) it should be taken care of by your mpi compiler (mpif90). Most likely your environment is set up incorrectly or you ...

robertson

It also looks like you're compiling with the Intel Fortran compiler but trying to link with a NetCDF compiled with GNU (highlighted in red ). /work/apps/intel/mvapich2/2.3.2/bin/mpif90 -fp-model precise -ip -O3 -traceback -check uninit -assume byterecl -I/work/users/weather/user/manh/COAWST/Lib/MCT ...

robertson

We need to see the command that came right before all your undefined references. Also, do you have "USE_NETCDF4" set to on your build_roms.sh?

robertson

Where are your libarpack.a and libparpack.a ? Assuming your ARPACK source code is in the /root/ARPACK directory then both libarpack.a and libparpack.a should be in /root/ARPACK. The way you have things configured, you are telling the linker that libparpack.a is in the /root/ARPACK/PARPACK directory ...

robertson

I also just noticed that it looks like you have edited the build script and my_build_paths files with a windows editor that uses incorrect line returns (those \r warnings). That could have been causing the error you had originally. When I look at your build_roms.bash with an editor like vim I see ...

robertson

Did you build NetCDF yourself or use the NetCDF (and NetCDF fortran) provided by Cygwin? From you error messages it looks like you built netcdf fortran but not the required Netcdf-C. I would suggest installing the cygwin provided netcdf and netcdf-fortran.

robertson

We need the linking command that precedes the errors you posted. It should be a multi-line command listing all the built libraries that will makeup the executable...something similar to this: /opt/sw/packages/intel/17.0.4/compilers_and_libraries/linux/mpi/intel64/bin/mpiifort -fp-model precise -heap ...

robertson

The typos in the roms.in glossaries were corrected in SVN Revision 1009 and Git cbc84128d7d33150dc40ade4821b82dce6ce5662. Details can be found

here

robertson

Fixed in SVN Revision 1009 and Git cbc84128d7d33150dc40ade4821b82dce6ce5662. Details can be found

here

robertson

idDtrc is "typed" and allocated in mod_ncparam. Check the mod_ncparam.f90 file in your /projappl/project_2000339/source/waom/Build directory. There should be a block like this: ! ! Tracer/Momentum Diagnostic variable IDs. ! integer, allocatable :: idDtrc(:,:) ! tracers terms integer, allocatable ...

robertson

In your Build_roms directory, what do lines 190-200 of your close_io.f90 file look like? Be sure to paste the lines inside a [code][/code] block so we can count white spaces. Also, what revision number of ROMS are you using and what compiler?

robertson

Are you sure that the grid file is at /home/cyue/cyue/bohai/data? It looks like your username (cyue) is doubled in there.

robertson

Please attach your gbplume.h file where your chosen CPP Definitions are set.

robertson

The problem is the version of cpp that comes with Xcode. It's likely that Homebrew (I know Macports does) has a working cpp you can use instead. I would suggest you: Make a ~/Compilers/ROMS directory (mkdir -p ~/Compilers/ROMS) Place a copy of the Darwin-gfortran.mk file from the Compilers directory ...

robertson

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robertson

The "Permission denied" error would suggest that your user does not have read and/or write permissions to the file or directory.

The command "ls -la" will give you the permissions of all the files and the current directory, which will be listed as a single period (.)

robertson

Hello, Check the timestamp on your oceanM or oceanG perhaps your build failed and the executable is an older one from an upwelling test case. Though I don't believe this is contributing to your issue, you might consider setting MY_PROJECT_DIR to ${PWD} so your executable is always written to the ...

robertson

Once you switch to Ubuntu, the plotting package will look for Linux-gfortran.mk not CYGWIN-gfortran.mk. Also, I would suggest a switch to using the build script (src/Bin/build_plt.{sh|bash}) so you don't have to modify the Linux-gfortran.mk file directly.

robertson

The directory you listed looks to have all the libraries you need in the same directory. Is the nf-config you're using associated with that lib directory you listed? I would guess not since the output of "nf-config --flibs" has different directories for libnetcdff and libnetcdf.

robertson

There are a couple oddities about your 'nf-config --flibs' output. First, "-O" and "-tp p7" are compiling flags, not linking flags. That would suggest that perhaps NetCDF wasn't configured/compiled quite right. Second, why is -R (I believe being treated as -rpath in this case) used for the C library ...

robertson

If your configure line is a copy and paste of what you're actually using then most likely you need to add some spaces and change both 'l's to 'I's in the CPPFLAGS. ./configure CPPFLAGS='-I/home/maziar/Downloads/q/hdf5-1.8.9/include -I/home/maziar/Downloads/q/zlib-1.2.7/include' LDFLAGS='-L/home ...

robertson

From the flags it appears that you have enabled gfortran but my first guess is that either gfortran is not installed or is not in your path. Most modern Linux distributions have a separate package for the GNU fortran compiler; it no longer comes as part of the gcc package. I believe Ubuntu has many ...

robertson

Check the permissions on your /home/survstu1/ROMS/trunk/Projects/Upwelling/Build_roms directory. Your error would indicate that you don't have the proper permissions to write to that directory. However, it is strange that /usr/bin/cpp appears to be able to create the /home/survstu1/ROMS/trunk ...

robertson

I'm not positive with newer versions of PGI but with older versions you have to run the makelocalrc script (as root so you'll still need to ask the system manager) every time gcc is upgraded. In your case the system manager logged in as root should be able to run the following: cd /home/software/pgi ...

robertson

Hi, I think we need clarification and/or more information. You mention segmentation fault but the post you refer to is a compiler linking error. If you are getting the same error as the post you refer to, it is likely that you have not set USE_NETCDF4 (and possibly the appropriate NETCDF_CONFIG and ...

robertson

Scientific Programmer Needed Integrated Statistics is looking for a Scientific Programmer to work with the USGS Coastal and Marine Geology Program at the Woods Hole Coastal and Marine Science Center in Woods Hole, MA. USGS earth scientists explore and study many aspects of the underwater areas ...

robertson

First thing I would check is that your process (oceanS) is not constantly switching cores on your machine. I don't know a good way to do this with oceanS but I would suggest compiling with Open MPI then run with one processor and enable the --bind-to-core (or equivalent memory affinity option for ...

robertson

Dear all, The first repair of the server that hosts myroms.org was only partially successful. The damaged caused by a faulty uninteruptable power supply (UPS/battery backup) was more extensive than originally thought. On Tuesday July 10th, the server's motherboard was replaced and the server booted ...

robertson

The NetCDFs on the system are almost certainly compiled with gcc/gfortran. You are trying to compile ROMS with the Intel compiler. You need to either use gfortran to compile ROMS or compile NetCDF with the Intel compiler. If you don't have the Intel C compilers you can use gcc for the C compiler and ...

robertson

The two issues should not have anything to do with each other. svn: Can't read file 'ROMS_620/Lib/ARPACK/LAPACK/.svn/log': Permission denied Appears to be a file permission error. Check the permissions on that file and make sure your user and/or group have write permissions on that file. Perhaps ...

robertson

Are you sure that the computer you are running svn on has access to the internet? Some clusters and computer centers don't allow their high performance computers access to the internet for security and performance reasons.

robertson

This topic is far too long so I am locking it. Please create new posts for future queries related to this topic.

robertson

Posted at the request of Villy Kourafalou. Dear colleagues, On behalf of the session 6 organizers, I would like to invite you to submit an abstract for the TOS/ASLO/AGU 2012 Ocean Sciences meeting, 20-24 February, 2012 , Salt Lake City, Utah, U.S.A.. https://www.sgmeet.com/osm2012/default.asp ...

robertson

Please check the config.log file to see the actual error that is occurring and report back.

robertson

In your case that line should have been:

svn co --username LRasmuson https://www.myroms.org/svn/src/trunk my_dir

because user names are case sensitive.

Sorry for the confusion.

robertson

If you need to specify a user name you should do it like this:

svn co --username lrasmuson https://www.myroms.org/svn/src/trunk my_dir

Putting it in the URL will not work.

Dave

robertson

This thread was getting off topic so I moved the discussion about optimization flag errors to a new thread: https://www.myroms.org/forum/viewtopic.php?t=2180 Please use the above topic for discussion related to ifort optimization flag issues on Intel i7 machines and reserve this topic for ...

robertson

I refer you to the following topic:

viewtopic.php?t=872

Please let us know if that solves your problem.

robertson

The build.bash script is telling you that the directory /home/aliayamahdi/roms/trunk does not exist. The script is trying to change in to the directory you set for MY_ROMS_SRC in your build.bash script. Double check that you have set this correctly and that it contains the ROMS source codes.

robertson

Ph.D. Student Opportunity Population Connectivity / Ocean Modeling MIT/WHOI Joint Program We are looking for a highly motivated Ph.D. student to join a team of scientists in the Biology Department at WHOI to work on modeling marine population connectivity in a tropical ecosystem. Research will ...

robertson

On line 35 of src/Utility/slevels.F you need to remove " , tindx " from the end of that line so it reads: integer file, nc_gid This doesn't phase most compilers but gfortran is quite picky about types. This typo will probably be fixed soon, but for now you can correct it yourself. The error is ...

robertson

Did you compile the ncarg libraries your self? or did you get them from a binary package? It's possible that the ncarg libraries you have on your machine are not compatible with your SUN f95 compiler. You may need to compile ncarg with the same compiler(s) you are compiling the ROMS plotting package ...

robertson

Sometimes gfortran is not called gfortran, sometimes it's something like gfortran44 for gfortran version 4.4.x. You need to find out what gfortran is actually called on your machine and use that name when making the adjustment Kate mentioned.

robertson

This is usually due to your computer time clock not being synced with remote computer that is storing your source code. If you are in a Linux environment, look in to running ntpd on both/all machines to keep your clocks synced. This warning can be ignored if you do make clean before make or use the ...

robertson

A question and a suggestion. Question(s): Do your Linux cluster compute nodes have AMD Opteron processors? If not, you should take out the ' -tp k8-64 ' flag or replace the 'k8-64' with a more appropriate value. Even if they are Opterons, you might get better performance with 'k8-64e' Check the man ...

robertson

On the files that are listed as modified, do an svn diff , i.e. svn diff makefile , to see how they differ from the original files on the myroms.org svn server. Perhaps your makefile or build script has somehow become corrupted. You might also want to make sure that all the files are in unix format ...

robertson

What have you set ROMS_APPLICATION and FORT to and what do you get from the following commands: uname -s | sed 's/[\/ ]/-/g' uname -m | sed 's/[\/ ]/-/g' Also, what does svn status in your root source code directory tell you? do you have any files marked with a ' C '. If so you have some unresolved ...

robertson

I would suggest reading the

ROMS 3.3 release notes. There is mention of changes to ana_psource.h involving Lsrc. If you are using customized analytical functions you may need to update them to reflect this change.

robertson

Did you compile NetCDF yourself or install it as a package? In most cases it is easier and almot always necessary to compile NetCDF with the same compiler and options you wish to compile ROMS with. In short, unless you can find out exactly how your NetCDF was configured and compiled your first step ...

robertson

I have absolutely no idea why this post was lost but I was able recover it. Thank you Kate for pointing this out.

robertson

What version of NetCDF did you compile with this version of the PGI compiler and what flags did you use? I am unable to build NetCDF-3.6.3 with PGI 5.1-6 and a simple google search reveals notes on building NetCDF-3.5.1 with the 5.1 compiler but no newer versions of NetCDF. The PGI 5.1 compiler had ...

robertson

As you have realized, the plotting packages is telling you that one of the files listed in your csec_upwelling.in file is missing. Do you have a copy of default.cnt in the directory where you are executing the : csec < csec_upwelling.in command? If not change that line in your csec_upwelling.in file ...

robertson

You might want to check if you have a newer PGI version available to you. I think you're using version 5.1-6 from 2004 ("PGF90/any Linux/x86 5.1-6: compilation aborted"). PGI is now at version 9; perhaps 5.1 doesn't handle the INTERFACE block correctly. However, it might be helpful if you attached ...

robertson

grep: illegal option -- P Usage: grep -hblcnsviw pattern file . . . ./build.bash : Unknown option [ 24 ] Available Options: -j [N] Compile in parallel using N CPUs omit argument for all avaliable CPUs -noclean Do not clean already compiled objects This grep error is due to the fact that your ...

robertson

42nd International Liege Colloquium on Ocean Dynamics Multiparametric observation and analysis of the Sea - First Announcement 26-30 April 2010 Web site: http://modb.oce.ulg.ac.be/colloquium/ The colloquium will provide a forum to present and discuss recent scientific advances on the use of new ...

robertson

As noted in the build.bash file just above the the lines you have pasted:

Any string value (including off) will evaluate to TRUE in conditional if-stamentents.

You must either comment out the USE_MPI and USE_MPIF90 lines or remove the word "off" on those lines.

robertson

Troy, So what then do the instructions: "set BPARNAM correctly and activate the corresponding CPP option" mean? BPARNAM is the location and name of your biology input parameters file. An example for EcoSim is can be found at ROMS/External/ecosim.in . I would suggest copying this file to your project ...

robertson

Make the extension txt or log

robertson

PGF90/x86-64 Linux 7.2-3: compilation aborted The above is not a path it's just the name of the compiler. but actually compilation path is /opt/pgi/linux86-64/7.2/bin. /opt/pgi/linux86-64/7.2/bin is a symbolic link to /opt/pgi/linux86-64/7.2-3/bin You problem doesn't have anything to do with ...

robertson

It looks like you have a couple problems: The build process should not be looking for ' pgi ' ('which pgi' from the error you posted), it should be looking for pgf90 . Did you modify FC in your Compilers/Linux-pgi.mk file? If so, change it back. when you set your NETCDF_INCDIR you put a space at the ...

robertson

That HDF5 version (1.6.6) is much to old to be used with NetCDF-4. Perhaps you have a new version in a different location?

robertson

The plotting package has been updated so that sec and cnt create plots with a white background and black foreground. See :arrow: this Trac ticket . csec and ccnt still take their background and foreground colors from the color palette you select in the .in script. Please update your code and ...

robertson

Trac System Upgraded to 0.11 We have upgraded Trac to the latest version. The most noticeable difference is that you will no longer have to log in to view tickets. You will still have to log in to browse the source, view the timeline etc. The login procedure has changed: Go to https://www.myroms ...

robertson

As noted

here, cnt and sec are contour only black and white versions of ccnt and csec. Have you tried using csec with one of the gray palettes? That should give you images without color.

Note: I just updated the wiki page to clarify this a bit.

robertson

What do you mean by "training dods.o3d.org"? What email address did you send your request to? The o3d.org server is not part of myroms.org so the user names and passwords for that server would be different. Please clarify what you are trying to do.

robertson

Hi, A couple things are happening here. First is the fact that your PMIN and PMAX values are way out of range. If you look at the output from the ccnt command you will see from the last frame that the values are between ~14.61 and ~15.97. I would suggest using 14 and 16 instead of -2.0 and 28. These ...

robertson

check near the bottom of the following thread:

viewtopic.php?f=14&t=589

robertson

check near the bottom of the following thread:

viewtopic.php?f=14&t=589

robertson

I would guess that you are exceeding your system's file size limit with your output files. If the history file is near 2GB at the time of the crash, try splitting your outputs into multiple files. Read: https://www.myroms.org/wiki/index.php/ocean.in#Output_Frequency_Parameters Specifically NDEFHIS ...

robertson

I don't know why you still don't have nf_test.exe. Are you sure make check completed successfully? Earlier in the ROMS compilation, netcdf.mod is copied from the NETCDF_INCDIR directory. One of three things is likely happening: When building NetCDF make install failed or was not executed Your NETCDF ...

robertson

First, in cygwin (and any UNIX like envronment) ls, by default, hides "dot" files. That means any file that starts with a "." will not show up with a standard 'ls' command. To see dot files you must type ' ls -a '; type ' ls --help ' for further info and options. Second, NetCDF has changed the way ...

robertson

MPICH2 is an MPI implementation. MPI is only used for distributed memory. For shared memory you will need to set USE_OpenMP in your build script . This will set the OpenMP flag for your compiler. I realize you don't wish to use NetCDF's parallel I/O but keep in mind that NetCDF Parallel I/O is only ...

robertson

This indicates that you are still compiling against NetCDF-3. Remember that any NETCDF/HDF5 paths you set in you makefile will override the ones in the Linux-ifort.mk file. Likewise, NetCDF/HDF5 paths set in your build script will override your makefile AND Linux-ifort.mk . If you are using the ...

robertson

I believe for Intel's MPI the executable is named mpiifort. What you'll want to do is turn on USE_MPIF90 Then edit your Compilers/Linux-ifort.mk file of you ROMS code. Around line 70 you will see: FC := mpif90 change this to: FC := mpiifort Then of course you'll want to make sure your PATH is set ...

robertson

That is because those pages don't exist yet. Any link on the wiki that appears in green is to a page that does not yet exist. When you click on a link to a page that does not exist in the wiki it automatically tries to create that page. However, at this point only a few users are allowed to edit ...

robertson

It appears that the mex file you're using ( /home/tiger/RNT/matlib/rnt/rnt_oa2d_mex.mexglx ) was compiled with the Intel Fortran compiler and you either don't have the Intel compiler or the lib directory for the Intel compiler is not in your library path. The error is telling you that rnt_oa2d_mex ...

robertson

I have not been able to reproduce your error but The errors I see in the Apache logs are below: [Fri Oct 31 04:59:00 2008] [error] [client 202.36.29.1] Provider encountered an error while streaming a REPORT response. [500, #0] [Fri Oct 31 04:59:00 2008] [error] [client 202.36.29.1] A failure ...

robertson

Question: Which Fortran compiler (if any) do you have on your system? You have told ROMS to build with g95 but g95 is not in your path ( which: no g95... ). If you don't have a Fortran 90 compiler in your path it is more than likely that your NetCDF library was built without the Fortran 90 interface ...

robertson

This is not an error, it is simply a report.

robertson

The coastline is not needed when plotting the upwelling test case. You should set CST to F in your .in file so the plotting package will ignore the 7th input file. I have tried to make this a little clearer in the tutorial. Sorry for the lack of clarity regarding the fort.35 file. There is not a ...

robertson

The 8th Workshop on Adjoint Model Applications in Dynamic Meteorology The Chateau Resort and Conference Center in Tannersville, Pennsylvania, USA, May 18-22, 2009 The 8th Adjoint Workshop will be held 18-22 May 2009 at The Chateau Resort and Conference Center in Tannersville, Pennsylvania, USA. As ...

robertson

As stated in the tutorial, you need to make sure that the same compiler is used for both NCAR Graphics (or NCL) and the ROMS plotting package. The following information was contained in the first google search result for '/usr/local/lib/libncarg_gks.a(gerlog.o):gerlog.f': It looks like you may be ...

robertson

Fifth WMO International Symposium on Data Assimilation 5-9 October, 2009, Melbourne, Australia The 5th WMO International Symposium on Data Assimilation will be convened in the Southern Hemisphere springtime, 5-9 October, 2009 in Melbourne, Australia. The goals of the Symposium are: To assess recent ...

robertson

The search feature should be fixed now. Thanks for reporting the problem and thanks to user ocecept for describing the problem in a way that allowed me find it and fix it.

robertson

The "contributions" tab at the top of each wiki page is where users can add notes or corrections to the wiki. Since I'm not sure what wiki page you are referring to (I'm guessing this one ) I can't make the correction/note. If you can navigate to the wiki page that needs the correction, click the ...

robertson

The College of Marine Science (CMS) at the University of South Florida (USF) invites applications for two tenure-track, nine-month academic faculty positions in Physical Oceanography. Appointments are expected to be at the Assistant Professor or Associate Professor rank. Salaries are negotiable and ...

robertson

I am not familiar with OpenMP but I would start by setting OMP_NUM_THREADS to 4 to match your 2x2 tiling. With 2x2 tiling you are telling ROMS to make 4 tiles but OpenMP will only give ROMS 2 threads if you have OMP_NUM_THREADS set to 2.

robertson

The problem is with you linker (ld). Use google to search for "ld unrecognized option as-needed" for possible causes and solutions.

Good luck

robertson

/shared/nagesh/gfortran/gcc-4.2/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.2.4/f951: error while loading shared libraries: libmpfr.so.1: cannot open shared object file: No such file or directory It's likely that gfortran you have installed was built with the MPFR library but you do not have that ...

robertson

The ROMS/Cygwin tutorial in the wiki has been changed to suggest using the command line subversion client within cygwin. Hopefully this will limit \r problems in the future.

https://www.myroms.org/wiki/index.php/ROMS_Cygwin

robertson

I have updated the tutorial in the wiki to suggest using the cygwin command line svn client. If you have already installed cygwin you can run the setup.exe again and grab any packages you may have missed. There are three more packages listed than before.

robertson

You're on the right trac about the wrong number of threads. I believe you need to edit the ROMS/External/ocean_upwelling.in . You chose to run on 4 processors (-np 4) but the bold part of this line: Tile partition information for Grid 01: 0041x0080x0016 tiling: 001x001 tells me that NtileI and ...

robertson

Have you tried compiling the model in serial (unset USE_MPI and USE_MPIF90 in your makefile) to make sure your Fortran compiler works? What Fortran compiler are you using? Based on your /usr/bin/cpp lines it looks like you're using g95 : /usr/bin/cpp -P -traditional -DMPI -DLINUX -DX86_64 -DG95 -D ...

robertson

Diagnostic information can be found by clicking "Model Diagnostics" in the left column of the main WikiROMS page.

robertson

Since WikiROMS is now our documentation I changed that link to point to WikiROMS. Unfortunately that diagnostics page didn't get added to the wiki. I will add it to the wiki soon, hopefully tomorrow.

robertson

First of all it is not recommended to check out code from tags directory because running svn update at a later date will not update your copy of the code with bug fixes or improvements. The versions in the tags directory are more of a time line of major achievements in ROMS history. It is recommend ...

robertson

I checked the logs and the only attempt I see from your user name to retrieve https://www.myroms.org/svn/src/trunk looks like it was made in a web browser. Have you been able to download the code via SVN in the past?

robertson

You can also download the move from the link below.

http://www.myroms.org/links/roms_project.mov

You may use this movie for any purpose you see fit as long as a) Rob Hetland is cited, and b) it is non-profit.

robertson

The initialization files for the BIO_TOY application are now on the datasets page.

robertson

Hi, The mismatch error you're seeing most likely points to Subversion being upgraded to 1.4.5 but some or all of the Subversion libraries not upgrading. How did you install subversion-1.4.5? Did you use a pre-compiled binary (RPM, Debian package, etc.) or did you compile from source. Was it ...

robertson

This post belongs in the ROMS Installation forum. I have posted my reply there. This topic is now locked. If you wish to post a reply do so here.

robertson

Presentations from the 2007 ROMS workshop at UCLA can be found here:

http://www.myroms.org/index.php?page=ROMS_2007_agenda

Electronic versions of the posters that were presented can be found here:

http://www.myroms.org/Workshops/ROMS200 ... s/posters/

robertson

I have looked at the svn and apache log files and it does not appear that user name pruthviraj has attempted to download the code, failed or otherwise. I can see your connections through a web browser. It could be a firewall or proxy server issue. SVN transmits data using the WebDAV protocol ...

robertson

2007 ROMS/TOMS User Workshop and Community Sediment Transport Modeling (CSTM) Meeting UCLA, Los Angeles, October 1-5, 2007 Please check the following link for a PDF of the final program. http://www.myroms.org/Workshops/ROMS2007/Program_2007.pdf Notice we a map of the UCLA campus to help you get to ...

robertson

USF Research Associates (post-doctoral) (12566 & 12567) The College of Marine Science, University of South Florida, seeks two Research Associates (post-doctoral) (#12566 & #12567) in coastal ocean circulation modeling and analyses. Successful candidates will engage in a coordinated program of ...

robertson

I sent an email to all users with illegal characters (including spaces) in their user name several months back. Perhaps you missed it. please send an email to robertson@marine.rutgers.edu containing what you would like you new user name to be.

robertson

Hi, The issue with the configure script seems to be that ifort for windows likes to build object files with the .obj extension instead of the usual .o so the tests in the configure script can't find the resulting compiled files. My first idea was to change the OBJEXT variable to 'obj' but that ...

robertson

Your ROMS user name is George with a capital "G".

Code: Select all

svn checkout --username George https://www.myroms.org/svn/src/trunk my_roms_dir

Dave

robertson

Your user name is Povl (Capital P lower case ovl)and the error in the logs is password mismatch. Since you were able to log in to the forum to post your question, you must know you password. Perhaps you are typing it incorrectly. Remember that your password to access the svn repository is the same ...

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