Michael, Could you please try h5check tool to see if file is corrupted?
We are in the process of releasing a new version of h5check, so there is no an officially released tar ball yet. Please grab the code from ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/epourmal/h5check.tar Elena On Mar 30, 2010, at 11:35 AM, Michael Dietze wrote: > >> Message: 5 >> Date: Mon, 29 Mar 2010 19:12:51 -0600 >> From: "George N. White III" <[email protected]> >> To: HDF Users Discussion List <[email protected]> >> Subject: Re: [Hdf-forum] R hdf5 package error >> Message-ID: >> <[email protected]> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> On 3/29/10, [email protected] <[email protected]> wrote: >>> >>> I was wondering if anyone has experience with the hdf5 package for the R >>> statistical software. Right now we can get the code to compile and while >>> it usually reads existing hdf5 files it doesn't write hdf5 files that can >>> be read by itself or other software. >>> >>> We have tried installing this on various Linux machines (both Red Hat and >>> Ubuntu) by using both the package managers and compiling the code from >>> scratch. We've compiled using both HDF5 1.8 and 1.6 and neither works. >> >> We use R routinely with files converted using h4toh5, but 99% of the time we >> use hdf5load. We try to use the platform's hdf5 library, which in our case >> is >> 1.6 on Ubuntu and 1.8 via macports on MacOSX. >> >> There have been versions of the R hdf5 library for Ubuntu, but some versions >> abort when they encounter elements in the hdf5 that aren't supported. Our >> files have such elements but the information is redundant, so we patch the >> library to omit the unsupported elements. >> >> Have you run "example(hdf5save)" successfully? > > Yes, that runs fine. In fact, as long as we don't quit out of R we can > both read and write files, but if we quit and restart R then we can no > longer read the files we just wrote and were able to read a second ago. > >>> Specifically, this simple test in R produces the following error >>> >>> Step 1: create file (run from within R) >>> >>> library(hdf5) >>> data = 1:10 >>> hdf5save("test.h5","dat") >> >> did you mean: hdf5save("test.h5","data") > > That's a typo...just in the email, not in what I've been running -- I > actually meant for both to be "dat" > >>> >>> Step 2: exit and then restart R >>> >>> hdf5load("test.h5") >>> >>> HDF5-DIAG: Error detected in HDF5 library version: 1.6.6 thread >>> 47700932800864. Back trace follows. >>> #000: H5F.c line 2049 in H5Fopen(): unable to open file >>> major(04): File interface >>> minor(17): Unable to open file >> >> This looks more like a permission problem. If you change the filename to >> "/tmp/test.h5" do you get the same error? > > yes I get the same error > > I also checked that I do have read/write permissions for the file. In > addition from outside R I ran > > h5dump test.h5 > > which returned > > h5dump error: unable to open file "test.h5" > > An additional odd bit of info is that we do have one computer that runs > an older version of Ubuntu where the library has worked for a long time > and we only discovered this error when our sysadmin tried putting this > on our Redhat cluster. Even when we download the same exact version of > hdf5 and the R hdf5 library that is on the machine that does work we > still can't get things to work. We also found that on our newer Ubuntu > machines that the version that comes from the Synaptic package manager > doesn't work either. > > We are just storing vectors of floats so the data format is nothing odd > that should be hard to read or write. > > Also, for what it's worth, I tried contacting the author of the R hdf5 > package about a week ago and got no response. > >>> #001: H5F.c line 1829 in H5F_open(): unable to read superblock >>> major(04): File interface >>> minor(24): Read failed >>> #002: H5Fsuper.c line 114 in H5F_read_superblock(): unable to find file >>> signature >>> major(04): File interface >>> minor(19): Not an HDF5 file >>> #003: H5F.c line 1281 in H5F_locate_signature(): unable to find a valid >>> file signature >>> major(05): Low-level I/O layer >>> minor(29): Unable to initialize object >>> Error in hdf5load("test.h5") : unable to open HDF file: test.h5 >> >> >> -- >> George N. White III <[email protected]> >> Head of St. Margarets Bay, Nova Scotia >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org >> >> >> End of Hdf-forum Digest, Vol 9, Issue 55 >> **************************************** > -- > ________________________________________________________________________ > Michael Dietze [email protected] > Assistant Professor www.life.uiuc.edu/dietze > Department of Plant Biology (217) 265-8020 > University of Illinois 1405 IGB / 183 Morrill > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org _______________________________________________ Hdf-forum is for HDF software users discussion. 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