Greetings Chad! > Sean, > > I just got HDF5 to support, but there is no "make install:" option. `make install` should work - did you follow the instructions at http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL regarding the ./configure setup? > Where do I put it so that when I compile netCDF again, it can find > what it needs. Can I just copy everything in the HDF5/bin folder to > /usr/local/bin, or maybe I should make it /usr/local/hdf5/bin. Are > there any library or include files that need to go into > /usr/local/hdf5? I figure if I use a separate pat like > /usr/local/hdf5/bin, and then add that to my $PATH or remove it from > my $PATH, I should be able to compile netCDF with or without HDF5 > support. It would be easier if there was an environmental variable > that the netCDF compile script recognized, like > export HDF5=/usr/local/hdf5. Would that work? The configure script for netCDF4 includes an option --with-hdf5=<path to top level hdf5>. If you run the config script for hdf5 using --prefix=<path where you want hdf libs, bin, and include to go>, then simply use this path when you compile netCDF4. For example, you suggested /usr/local/hdf5 as a place to stuff hdf5. In that case, when configuring the build for hdf5, use ./configure --prefix=/usr/local/hdf5 [other options, as needed] Then, when compiling netCDF, use: ./configure --with-hdf5=/usr/local/hdf5 [other options, as needed] > That way I could > enable or disable that variable for compiling netCDF with or without > HDF5 support. > Changing $PATH as needed should work for what you need - just make sure to keep close watch on what $PATH says because it can bite pretty hard. > <paste> > > I do not know why /bin/sh points to dash by default. That is weird. > I just tried an apt-get install bash, and it says I have the latest > version. I double-checked this by typing > > address@hidden:/bin$ whereis bash > bash: /bin/bash /etc/bash.bashrc /usr/share/man/man1/bash.1.gz > > So, /bin/bash is the real bash. Should I change the symbolic link so > that /bin/sh points to /bin/bash? Would that help? I do not know why > /bin/sh points to dash instead of bash. Any idea? Seems stupid to > me. I am going to go ahead and rm /bin/sh and point it to /bin/bash > instead. > The Ubuntu devs decided to make /bin/dash the default, and I am not sure of why they chose to do so. Does the Intel ifortvars.sh start with #!/bin/sh? If so, then that explains everything, as /bin/sh points to /bin/dash, and therefore /bin/dash was being used to run the script even though you are running /bin/bash. > I just tried your idea and I think it worked. When I ran a make > -check, it says it passed all the tests. I will attach log files for > you to double check. Things look good to me. > > I do not have HDF5 compiled on this machine, because address@hidden told > me not to. But, I do have a compiled version of netCDF 363 (borrowed > the binaries from a CentOS server at the university). So, I will have > to keep both netCDF 4 without HDF5 for compiling WRF and doing WRF > simulations and need to keep netCDF 4 with HDF5 suport, for using > nccopy to convert the WRF output data into a format with HDF5 that > Tecplot can read. As long a we can get netCDF to compile with HDF5, > then I should be in good shape. Thanks for telling me about nccopy. > Saves me a bunch of time so I do not have to write a custom data > converter. Incidentally, I did ask the WRF people about their plans > regarding support for netCDF4 with HDF5 support and they said its at > least a year away. > > Now I need to re-compile it with HDF5. Can I use pre-compiled > binaries, or should I compile HDF5 with the intel compilers to make > sure that its fully compatible? There are linux 64 bit binaries of > HDF5 available at > > http://www.hdfgroup.org/HDF5/release/obtain5.html > > I am leaning toward trying to compile HDF5 first. I know that WRF > will not compile unless its compiled under the same OS with the same > compilers. Is it the same for netCDF and HDF5? > > I am attaching logs of configure, make and make check. Tell me if the > little trick in switching /bin/sh -> /bin/bash actually worked. > > I have one important question. I just compiled netCDF 4.1.2 without > HDF5 support, and now want to compile WRF using it. If I have nccopy > from a netCDF 4.1.2 compilation with HDF5 support, will nccopy still > work, converting a WRF output file from 4.1.2 to 4.1.2 with HDF5 > support, or does nccopy only work for converting from netCDF 3.x to > netCDF 4.x with HDF5 support? > When you configured netCDF4, did you specify --enable-netcdf-4? If so, then I think nccopy will work. Sean > > Thanks, > > Chad > > On Thu, Jun 2, 2011 at 2:47 PM, Unidata netCDF Support > <address@hidden> wrote: > > Chad, > > > >> Sean, > >> > >> I am using the atest ubuntu 11.0.4, just downloaded and installed las > >> week. ÂHere is the ouput you requested: > >> > >> address@hidden:~$ echo $SHELL > >> /bin/bash > >> address@hidden:~$ ls -la /bin/sh > >> lrwxrwxrwx 1 root root 4 May 25 21:07 /bin/sh -> dash* > >> address@hidden:~$ > > > > The failures you get for `make check` show up when using ifort during the > > tests, and once again ifort is having issues finding the Intel shared > > objects. Just out of curiosity, is /bin/bash also a symlink to /bin/dash? > > If so, then that is the problem - dash is not 100% compatible with bash, > > and thus the Intel scripts may not be fully functional. If it is a link to > > dash, use apt-get to install bash and then try to rebuild. > > > >> > >> I am not sure if I should open a separate support issue for this, but > >> I am running into a data incompatibility problem. ÂI want to use > >> Tecplot 360 (tecplot.com) for visualzing and making movies of output > >> from WRF. ÂTecplot 360 support HDF5 data, but WRF only suports netCDF > >> without HDF5, from what I have read and been told by wrfhelp. ÂHow can > >> I get my data into Tecplot 360 from a netCDF file that has no HDF5? > >> Do you know if WRF planps to upgrade to HDF5 support soon? > > > > I am not sure what the plans are with WRF,as it is not developed at > > Unidata. The folks at NCAR who are involved in the administration of the > > codebase should be able to answer that question (I'd check with WRFhelp). > > The questions to ask would be if/when WRF plans to use netCDF4. > > > >> > >> I suppose we would need to get this netCDF 4 with HDF5 support to > >> compile, then I could write a program that read the netCDF without > >> HDF5 data, then wrote it back with netCDF with HDF5. ÂIs netCDF 4 with > >> HDF5 backwards compatible with output from say netCDF 363? ÂSo, if I > >> write a code using netCDF4 with HDF5, can I read netCDF 363 data and > >> then write it back in HDF5 format? > > > > netCDF4 will read data written with netCDF3 - no problems :-) That said.. . > > > >> Do you guys have any utiities that > >> already do this? ÂA simple utility that reads in a netCDF 363 data > >> file and upgrades it to netCDF4 with HDF5 support? ÂIf you do not, you > >> should write one. ÂIt would be simple for you guys that know netCDF so > >> well. Â If I have to do it, its going to take me a while to figure out > >> how.... time I really do not have right now. > > > > If you check out the netCDF FAQ > > (http://www.unidata.ucar.edu/software/netcdf/docs/faq.html), there is an > > entry about how to do this > > (http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#fv13). > > > >> I can write code in > >> Fortran and C, but would prefer to use Python. ÂPython can usually > >> call C libraries, so do you know for sure if Python can link to > >> netCDF4 with HDF5 support? > > > > Since nccopy can do what you need it to do (once we get it to compile, that > > is), it may be of general interest to know that there is a netCDF4 python > > wrapper that is functional, although a few features are missing (see > > http://code.google.com/p/netcdf4-python/). I've compiled and used this on > > MacOSX and it works great so far. > > > > Sean > > > >> If you can think of any other solution to > >> this problem, please let me know. > >> > >> > >> Many Thanks, > >> > >> Chad > >> > >> On Wed, Jun 1, 2011 at 3:03 PM, Unidata netCDF Support > >> <address@hidden> wrote: > >> > Hi Chad, > >> > >> > >> > >> Iatest ubuntu 11.0.4, just downloaded and installed las week. ÂHere is > >> the ouput you requested: > >> > >> address@hidden:~$ echo $SHELL > >> /bin/bash > >> address@hidden:~$ ls -la /bin/sh > >> lrwxrwxrwx 1 root root 4 May 25 21:07 /bin/sh -> dash* > >> address@hidden:~$ > >> > >> I am not sure if I should > >> > >> > >> On Wed, Jun 1, 2011 at 3:03 PM, Unidata netCDF Support > >> <address@hidden> wrote: > >> > Hi Chad, > >> > > >> > It seems as though netCDF is still having issues finding the Intel libs. > >> > First, which version of Ubuntu are you running? Second, could you send > >> > me the output from the following two commands: > >> > > >> > 1) echo $SHELL > >> > > >> > 2) ls -la /bin/sh > >> > > >> > Thanks! > >> > > >> > Sean > >> > > >> >> Hi Sean, > >> >> > >> >> I did as you suggested. ÂI cleared all the shell environmental > >> >> variables and used > >> >> source /opt/intel/bin/iccvars.sh intel64 > >> >> source /opt/intel/bin/ifortvars.sh intel64 > >> >> > >> >> The configure and make seemed to go ok, but when I ran "make check" it > >> >> failed 4 out of 5 of the tests. > >> >> > >> >> I made log files of each stage and attached them to this email for you > >> >> to examine. ÂDo you think gc/gortran would work better or stay with > >> >> intel on ubuntu? ÂOthers here at ASU reported better success with > >> >> intel compilers, which is why I am using them. > >> >> > >> >> > >> >> Thanks, > >> >> > >> >> Chad > >> >> > >> >> > >> >> On Tue, May 31, 2011 at 1:00 PM, Unidata netCDF Support > >> >> <address@hidden> wrote: > >> >> > Greetings Dr. Coulliette! > >> >> > > >> >> >> Hello, > >> >> >> > >> >> >> My name is Dr. Chad Coulliette. ÂI am working with Professor Alex > >> >> >> Mahalov at Arizona State University. ÂI have been trying to compile > >> >> >> netCDF on Ubuntu Linux 64-bit. ÂThe hardware is a MacBook Pro with a > >> >> >> Intel Duo Core 64-bit processor. ÂI want to compile and use WRF, but > >> >> >> need netCDF first. ÂI have netCDF installed as a package using > >> >> >> synaptic, but I suspect there is something deficient about it, so we > >> >> >> have been trying to compile and install netCDF from source code. ÂI > >> >> >> have netCDF-4.1.2 and have tried with both GNU compilers and Intel > >> >> >> compilers. ÂThe GNU compilers seem to compile ok....no errors during > >> >> >> make, but when I run "make check" it finds problems, and the message > >> >> >> actually says to contact this email address. > >> >> > > >> >> > From looking through the make-gcc.log, you seem to be using the Intel > >> >> > fortran compiler `ifort` along side the gcc `cc` compiler - this is > >> >> > because .configure could not find any other fortran compiler (i.e. > >> >> > gfortran) in your $PATH. The error you are getting, as indicated in > >> >> > the make-test-gcc.log file, is due to problems finding the Intel > >> >> > shared objects. This is probably because when you building with a GNU > >> >> > environment in mind and so you didn't source ifortvars.sh. If you > >> >> > want to go the GNU route, try installing gfortran . > >> >> > > >> >> >> With the Intel > >> >> >> compilers, it crashes during the make. ÂI included log files of the > >> >> >> configure, make and make check for the GNU compilers, and included > >> >> >> log > >> >> >> files for the configure and make for the Intel compilers. > >> >> >> > >> >> >> For the Intel compiler, I have been following the instructions at > >> >> >> > >> >> >> http://software.intel.com/en-us/articles/performance-tools-for-software-developers-building-netcdf-with-the-intel-compilers/ > >> >> >> > >> >> >> Are these the best compile instructions? ÂThey might be too old, > >> >> >> because I noticed a complaint about the compiler flag -xT being > >> >> >> depreciated. ÂI tried to take it out and run everything over, but > >> >> >> the > >> >> >> results were the same. > >> >> >> > >> >> > > >> >> > The instructions above are for an older version of netCDF. I would > >> >> > check out the Unidata netCDF docs, which can be found here: > >> >> > > >> >> > http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-install/Building-on-Unix.html#Building-on-Unix > >> >> > > >> >> > These docs do not specifically look at using the Intel compiler, but > >> >> > it should give you some general reference. > >> >> > > >> >> > What happens if you do not set any flags by hand, but only source > >> >> > iccvars.sh and ifortvars.sh before building? > >> >> > > >> >> > Cheers! > >> >> > > >> >> > Sean Arms > >> >> > > >> >> >> Could you examine the log files and let me know what to do? > >> >> >> > >> >> >> > >> >> >> > >> >> >> Thanks, > >> >> >> > >> >> >> Chad > >> >> >> > >> >> >> > >> >> > > >> >> > > >> >> > Ticket Details > >> >> > =================== > >> >> > Ticket ID: YWP-403246 > >> >> > Department: Support netCDF > >> >> > Priority: Normal > >> >> > Status: Open > >> >> > > >> >> > > >> >> > >> >> > >> > > >> > > >> > Ticket Details > >> > =================== > >> > Ticket ID: YWP-403246 > >> > Department: Support netCDF > >> > Priority: Normal > >> > Status: Open > >> > > >> > > >> > >> > > > > > > Ticket Details > > =================== > > Ticket ID: YWP-403246 > > Department: Support netCDF > > Priority: Normal > > Status: Open > > > > > > Ticket Details =================== Ticket ID: YWP-403246 Department: Support netCDF Priority: Normal Status: Open
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