# help with errors **URL:** \ **Category:** Hdf-forum archives\ **Created:** [November 4, 2011, 12:04am UTC](https://forum.hdfgroup.org/t/help-with-errors/2379 "2011-11-04T00:04:46Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Zaak\_Beekman](https://forum.hdfgroup.org/user_avatar/forum.hdfgroup.org/zaak_beekman/32/1829_2.png) [@Zaak\_Beekman](https://forum.hdfgroup.org/u/Zaak_Beekman)\ **Post date:** [November 4, 2011, 12:04am UTC](https://forum.hdfgroup.org/t/help-with-errors/2379/1 "2011-11-04T00:04:46Z")
Hi, The following piece of Fortran code is producing some cryptic errors i am having trouble understanding. The errors are attached as an attachment.        CALL h5dcreate\_f(newfl\_id, & >                         '/aux/planes/foo', & >                         H5T\_NATIVE\_DOUBLE, & >                         hifstate(n)%flspace,hifstate(n)%dset\_id(1),err) newfl\_id is of type INTEGER(HID\_T) and was return by h5fcreate\_f and is still open. The groups /aux and /aux/planes have already been created. hifstate(n)%flspace has been created by h5screate\_simple\_f and is of type INTEGER(HID\_T), and hifstate(n)%dset\_id(1) is of type INTEGER(HID\_T). Do /aux and /aux/planes need to be open? Could this be the issue? (Although I am using an absolute path so I don't think this is the issue) Thanks for any feedback, I am really stuck. Izaak Beekman [error.txt](https://hdf-discourse-1.s3.amazonaws.com/original/1X/c17770f4baec64a825cfbce5b5cb5bccd79acc82.txt) (68.8 KB) > **···** > > =================================== > (301)244-9367 > Princeton University Doctoral Candidate > Mechanical and Aerospace Engineering > ibeekman@princeton.edu > > UMD-CP Visiting Graduate Student > Aerospace Engineering > ibeekman@umiacs.umd.edu > ibeekman@umd.edu ---
**Author:** ![Izaak\_Beekman](https://forum.hdfgroup.org/user_avatar/forum.hdfgroup.org/izaak_beekman/32/864_2.png) [@Izaak\_Beekman](https://forum.hdfgroup.org/u/Izaak_Beekman)\ **Post date:** [November 4, 2011, 12:21am UTC](https://forum.hdfgroup.org/t/help-with-errors/2379/2 "2011-11-04T00:21:37Z")
Also, I am using HDF5-1.8.5-p1 on RHEL5 x86\_64, with intel's ifort 11.1 compiler, Build 20090630 Package ID: l\_cprof\_p\_11.1.046 and mvapich-1.1.0-qlc. I built HDF5 using this toolchain. Hi, > The following piece of Fortran code is producing some cryptic errors i am > having trouble understanding. The errors are attached as an attachment. > >        CALL h5dcreate\_f(newfl\_id, & > > >                         '/aux/planes/foo', & > >                         H5T\_NATIVE\_DOUBLE, & > >                         hifstate(n)%flspace,hifstate(n)%dset\_id(1),err) > > newfl\_id is of type INTEGER(HID\_T) and was return by h5fcreate\_f and is > still open. The groups /aux and /aux/planes have already been created. > hifstate(n)%flspace has been created by h5screate\_simple\_f and is of type > INTEGER(HID\_T), and hifstate(n)%dset\_id(1) is of type INTEGER(HID\_T). > > Do /aux and /aux/planes need to be open? Could this be the issue? > (Although I am using an absolute path so I don't think this is the issue) > > Thanks for any feedback, I am really stuck. Izaak Beekman [error.txt](https://hdf-discourse-1.s3.amazonaws.com/original/1X/c17770f4baec64a825cfbce5b5cb5bccd79acc82.txt) (68.8 KB) > **···** > > =================================== > (301)244-9367 > UMD-CP Visiting Graduate Student > Aerospace Engineering > ibeekman@umiacs.umd.edu > ibeekman@umd.edu ---
**Author:** ![epourmal](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/e/c67d28/32.png) [@epourmal](https://forum.hdfgroup.org/u/epourmal)\ **Post date:** [November 4, 2011, 12:52am UTC](https://forum.hdfgroup.org/t/help-with-errors/2379/3 "2011-11-04T00:52:38Z")
Izaak, There is a message in the error log file that object already exists.   #002: H5L.c line 1640 in H5L\_link\_object(): unable to create new link to object   #000: H5D.c line 170 in H5Dcreate2(): unable to create dataset   #006: H5L.c line 1675 in H5L\_link\_cb(): name already exists   #005: H5Gtraverse.c line 759 in H5G\_traverse\_real(): traversal operator failed     major: Symbol table     major: Dataset     minor: Callback failed     major: Symbol table     major: Symbol table     minor: Callback failed     minor: Unable to initialize object     major: Symbol table     major: Links     minor: Object already exists Elena > **···** > > On Nov 3, 2011, at 7:21 PM, Izaak Beekman wrote: > > > Also, > > I am using HDF5-1.8.5-p1 on RHEL5 x86\_64, with intel's ifort 11.1 compiler, Build 20090630 Package ID: l\_cprof\_p\_11.1.046 and mvapich-1.1.0-qlc. I built HDF5 using this toolchain. > > > > Hi, > > The following piece of Fortran code is producing some cryptic errors i am having trouble understanding. The errors are attached as an attachment. > > > >        CALL h5dcreate\_f(newfl\_id, & > >                         '/aux/planes/foo', & > >                         H5T\_NATIVE\_DOUBLE, & > >                         hifstate(n)%flspace,hifstate(n)%dset\_id(1),err) > > > > newfl\_id is of type INTEGER(HID\_T) and was return by h5fcreate\_f and is still open. The groups /aux and /aux/planes have already been created. hifstate(n)%flspace has been created by h5screate\_simple\_f and is of type INTEGER(HID\_T), and hifstate(n)%dset\_id(1) is of type INTEGER(HID\_T). > > > > Do /aux and /aux/planes need to be open? Could this be the issue? (Although I am using an absolute path so I don't think this is the issue) > > > > Thanks for any feedback, I am really stuck. > > > > # Izaak Beekman > > > > (301)244-9367 > > UMD-CP Visiting Graduate Student > > Aerospace Engineering > > ibeekman@umiacs.umd.edu > > ibeekman@umd.edu > > \\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Hdf-forum is for HDF software users discussion. > > Hdf-forum@hdfgroup.org > > [http://mail.hdfgroup.org/mailman/listinfo/hdf-forum\_hdfgroup.org](http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org) ---
**Author:** ![Izaak\_Beekman](https://forum.hdfgroup.org/user_avatar/forum.hdfgroup.org/izaak_beekman/32/864_2.png) [@Izaak\_Beekman](https://forum.hdfgroup.org/u/Izaak_Beekman)\ **Post date:** [November 4, 2011, 4:24pm UTC](https://forum.hdfgroup.org/t/help-with-errors/2379/4 "2011-11-04T16:24:48Z")
Elana, Thanks for the response. I am certain that this is the first call to create an object at this location with this name--but I am using collective calls to HDF5 routines and I have created the file collectively. Could this be an MPI related issue? The code that generates this error is fairly large, and it's not immediately obvious to me how to make a smaller code to reproduce this error. I commented out the call to h5dcreate\_f and replaced it with another one to create a data set, foo, under the root group which is also failing with the same errors. I'll re-double-check that the file has been created and opened correctly (i.e. collectively, etc.) and that I am not missing anything critical. Any additional thoughts about where I might have gone wrong are welcome. Izaak Beekman > **···** > > =================================== > (301)244-9367 > UMD-CP Visiting Graduate Student > Aerospace Engineering > ibeekman@umiacs.umd.edu > ibeekman@umd.edu > > On Fri, Nov 4, 2011 at 12:00 PM, \ wrote: > > > Send Hdf-forum mailing list submissions to > >        hdf-forum@hdfgroup.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > >        [http://mail.hdfgroup.org/mailman/listinfo/hdf-forum\_hdfgroup.org](http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org) > > or, via email, send a message with subject or body 'help' to > >        hdf-forum-request@hdfgroup.org > > > > You can reach the person managing the list at > >        hdf-forum-owner@hdfgroup.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Hdf-forum digest..." > > > > Today's Topics: > > > >   1. Re: help with errors (Elena Pourmal) > > > > ---------- Forwarded message ---------- > > From: Elena Pourmal \ > > To: HDF Users Discussion List \ > > Date: Thu, 3 Nov 2011 19:52:38 -0500 > > Subject: Re: [Hdf-forum] help with errors > > Izaak, > > > > There is a message in the error log file that object already exists. > > > >   #002: H5L.c line 1640 in H5L\_link\_object(): unable to create new link to > > object > >   #000: H5D.c line 170 in H5Dcreate2(): unable to create dataset > >   #006: H5L.c line 1675 in H5L\_link\_cb(): name already exists > >   #005: H5Gtraverse.c line 759 in H5G\_traverse\_real(): traversal operator > > failed > >     major: Symbol table > >     major: Dataset > >     minor: Callback failed > >     major: Symbol table > >     major: Symbol table > >     minor: Callback failed > >     minor: Unable to initialize object > >     major: Symbol table > >     major: Links > >     minor: Object already exists > > > > Elena > > On Nov 3, 2011, at 7:21 PM, Izaak Beekman wrote: > > > > Also, > > I am using HDF5-1.8.5-p1 on RHEL5 x86\_64, with intel's ifort 11.1 > > compiler, Build 20090630 Package ID: l\_cprof\_p\_11.1.046 and > > mvapich-1.1.0-qlc. I built HDF5 using this toolchain. > > > > Hi, > > > > > The following piece of Fortran code is producing some cryptic errors i am > > > having trouble understanding. The errors are attached as an attachment. > > > > > >        CALL h5dcreate\_f(newfl\_id, & > > > > > > >                         '/aux/planes/foo', & > > > >                         H5T\_NATIVE\_DOUBLE, & > > > >                         hifstate(n)%flspace,hifstate(n)%dset\_id(1),err) > > > > > > newfl\_id is of type INTEGER(HID\_T) and was return by h5fcreate\_f and is > > > still open. The groups /aux and /aux/planes have already been created. > > > hifstate(n)%flspace has been created by h5screate\_simple\_f and is of type > > > INTEGER(HID\_T), and hifstate(n)%dset\_id(1) is of type INTEGER(HID\_T). > > > > > > Do /aux and /aux/planes need to be open? Could this be the issue? > > > (Although I am using an absolute path so I don't think this is the issue) > > > > > > Thanks for any feedback, I am really stuck. > > > > # Izaak Beekman > > > > (301)244-9367 > > UMD-CP Visiting Graduate Student > > Aerospace Engineering > > ibeekman@umiacs.umd.edu > > ibeekman@umd.edu > > \\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Hdf-forum is for HDF software users discussion. > > Hdf-forum@hdfgroup.org > > [http://mail.hdfgroup.org/mailman/listinfo/hdf-forum\_hdfgroup.org](http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org) > > > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > > Hdf-forum is for HDF software users discussion. > > Hdf-forum@hdfgroup.org > > [http://mail.hdfgroup.org/mailman/listinfo/hdf-forum\_hdfgroup.org](http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org) ---
**Author:** ![Zaak\_Beekman](https://forum.hdfgroup.org/user_avatar/forum.hdfgroup.org/zaak_beekman/32/1829_2.png) [@Zaak\_Beekman](https://forum.hdfgroup.org/u/Zaak_Beekman)\ **Post date:** [November 8, 2011, 8:51pm UTC](https://forum.hdfgroup.org/t/help-with-errors/2379/5 "2011-11-08T20:51:01Z")
So, I it turns out I had sent the wrong error log. The correct error I am seeing is attached Again it is triggered on calls to h5dwrite\_f. The error has something about file locks. HDF5 is built against an MPICH variant and the intel compiler. The data is being read from and written to a lustre file system. I believe the all the tests passed when I installed HDF5-1.8.5p1 and I have been successfuly reading and writing data (collectively) in parallel until now. I spoke to our system administrator and he seems to think that if we remout lustrefs with different flags it will fix the issue, but both of us have limited experience. Has anyone seen these errors before? Is my sysadmin correct in saying that a simple change to the lustrefs mount flags will fix this? Many thanks again, Izaak Beekman [error](https://hdf-discourse-1.s3.amazonaws.com/original/1X/f22ab4c3e8430cef13292a5d46fe2613f3cfe099) (137 KB) > **···** > > =================================== > (301)244-9367 > Princeton University Doctoral Candidate > Mechanical and Aerospace Engineering > ibeekman@princeton.edu > > UMD-CP Visiting Graduate Student > Aerospace Engineering > ibeekman@umiacs.umd.edu > ibeekman@umd.edu ---
**Author:** ![robl](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/r/e9a140/32.png) [@robl](https://forum.hdfgroup.org/u/robl)\ **Post date:** [November 8, 2011, 9:17pm UTC](https://forum.hdfgroup.org/t/help-with-errors/2379/6 "2011-11-08T21:17:03Z")
It's good you found the correct error file. Your MPI version is a little on the older side. Newest versions have a bit more helpful error message: FPRINTF(stderr, "File locking failed in ADIOI\_Set\_lock(fd %X,cmd %s/%X,type %s/%X,whence %X) with return value %X and errno %X.\n"                   "- If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching).\n"                   "- If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option.\n", I don't have much personal experience with lustre, so I don't know the full ramifications of the 'flock' option, but that's what the lustre community tells me is needed. A more helpful error message is just one benefit of upgrading your MPI implementation. The Lustre driver has seen a host of improvements and bug fixes. If there's any way you can upgrade to MPICH2-1.4.1 or MVAPICH2-1.7, you will be a much happier lustre user. ==rob > **···** > > On Tue, Nov 08, 2011 at 03:51:01PM -0500, Zaak Beekman wrote: > > > So, > > I it turns out I had sent the wrong error log. The correct error I am > > seeing is attached Again it is triggered on calls to h5dwrite\_f. The error > > has something about file locks. HDF5 is built against an MPICH variant and > > the intel compiler. The data is being read from and written to a lustre > > file system. I believe the all the tests passed when I installed > > HDF5-1.8.5p1 and I have been successfuly reading and writing data > > (collectively) in parallel until now. > > I spoke to our system administrator and he seems to think that if we remout > > lustrefs with different flags it will fix the issue, but both of us have > > limited experience. > > > > Has anyone seen these errors before? Is my sysadmin correct in saying that > > a simple change to the lustrefs mount flags will fix this? > > -- > Rob Latham > Mathematics and Computer Science Division > Argonne National Lab, IL USA