h5py from install script on kraken
Hi everyone,
I just tried a new install of yt on kraken form the install script. It failed on installing h5py 1.3 with the following error:
****************************************** Configure: Autodetecting HDF5 settings... Custom HDF5 dir: /lustre/scratch/britton/local-dev Custom API level: None /opt/cray/xt-asyncpe/4.0/bin/cc: INFO: linux target is being used /opt/cray/xt-asyncpe/4.0/bin/cc: INFO: linux target is being used /lustre/scratch/britton/local-dev/lib/libhdf5.a(H5Zdeflate.o): In function `H5Z_filter_deflate': H5Zdeflate.c:(.text+0x134): undefined reference to `compress2' H5Zdeflate.c:(.text+0x1ee): undefined reference to `inflateInit_' H5Zdeflate.c:(.text+0x209): undefined reference to `inflate' H5Zdeflate.c:(.text+0x270): undefined reference to `inflateEnd' H5Zdeflate.c:(.text+0x3de): undefined reference to `inflateEnd' H5Zdeflate.c:(.text+0x410): undefined reference to `inflateEnd' /usr/bin/ld: link errors found, deleting executable `detect/vers' collect2: ld returned 1 exit status
Failed to compile HDF5 test program. Please check to make sure:
* You have a C compiler installed * A development version of Python is installed (including header files) * A development version of HDF5 is installed (including header files) * If HDF5 is not in a default location, supply the argument --hdf5=<path> ****************************************** error: command 'cc' failed with exit status 1
I checked that the kraken yt install from the yt module is using h5py 1.2, which I believe suffers from the h5py bug that was mentioned not too long ago. I double checked that I had gnu compiler module loaded, so I don't think that's it. Does anyone have any ideas?
Britton
This still seems to be an issue. Could someone just try running the latest install script on kraken to see if they get the same error?
Thanks, Britton
On Tue, Apr 19, 2011 at 11:20 PM, Britton Smith brittonsmith@gmail.comwrote:
Hi everyone,
I just tried a new install of yt on kraken form the install script. It failed on installing h5py 1.3 with the following error:
Configure: Autodetecting HDF5 settings... Custom HDF5 dir: /lustre/scratch/britton/local-dev Custom API level: None /opt/cray/xt-asyncpe/4.0/bin/cc: INFO: linux target is being used /opt/cray/xt-asyncpe/4.0/bin/cc: INFO: linux target is being used /lustre/scratch/britton/local-dev/lib/libhdf5.a(H5Zdeflate.o): In function `H5Z_filter_deflate': H5Zdeflate.c:(.text+0x134): undefined reference to `compress2' H5Zdeflate.c:(.text+0x1ee): undefined reference to `inflateInit_' H5Zdeflate.c:(.text+0x209): undefined reference to `inflate' H5Zdeflate.c:(.text+0x270): undefined reference to `inflateEnd' H5Zdeflate.c:(.text+0x3de): undefined reference to `inflateEnd' H5Zdeflate.c:(.text+0x410): undefined reference to `inflateEnd' /usr/bin/ld: link errors found, deleting executable `detect/vers' collect2: ld returned 1 exit status
Failed to compile HDF5 test program. Please check to make sure: * You have a C compiler installed * A development version of Python is installed (including header files) * A development version of HDF5 is installed (including header files) * If HDF5 is not in a default location, supply the argument--hdf5=<path>
error: command 'cc' failed with exit status 1
I checked that the kraken yt install from the yt module is using h5py 1.2, which I believe suffers from the h5py bug that was mentioned not too long ago. I double checked that I had gnu compiler module loaded, so I don't think that's it. Does anyone have any ideas?
Britton
Hi Britton,
This still seems to be an issue. Could someone just try running the latest install script on kraken to see if they get the same error?
I'll give it a shot.
Britton,
yes, I got the same error as you did. Some searching got me this:
https://trac.macports.org/ticket/28549
which pointed out that h5py-1.3.1 does not support hdf5-1.8.6. Does one of us want to try things with hdf5-1.8.5, or the development branch of h5py?
For those of you not on yt-dev, here is some context on the upgrade of hdf5 to 1.8.6:
http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2011-April/001234....
On Thu, Apr 28, 2011 at 12:03 PM, Stephen Skory s@skory.us wrote:
Britton,
yes, I got the same error as you did. Some searching got me this:
https://trac.macports.org/ticket/28549
which pointed out that h5py-1.3.1 does not support hdf5-1.8.6. Does one of us want to try things with hdf5-1.8.5, or the development branch of h5py?
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Stephen, nice job tracking that down. This is just another example of how hard it is keep yt easily installable everywhere.
Matt, that link refers to why we upgraded from h5py 1.2 to 1.3. Do you remember why we upgraded hdf5 to 1.8?
On Thu, Apr 28, 2011 at 1:12 PM, Matthew Turk matthewturk@gmail.com wrote:
For those of you not on yt-dev, here is some context on the upgrade of hdf5 to 1.8.6:
http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2011-April/001234....
On Thu, Apr 28, 2011 at 12:03 PM, Stephen Skory s@skory.us wrote:
Britton,
yes, I got the same error as you did. Some searching got me this:
https://trac.macports.org/ticket/28549
which pointed out that h5py-1.3.1 does not support hdf5-1.8.6. Does one of us want to try things with hdf5-1.8.5, or the development branch of h5py?
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
On Thu, Apr 28, 2011 at 1:39 PM, Britton Smith brittonsmith@gmail.com wrote:
Stephen, nice job tracking that down. This is just another example of how hard it is keep yt easily installable everywhere.
Matt, that link refers to why we upgraded from h5py 1.2 to 1.3. Do you remember why we upgraded hdf5 to 1.8?
To get symbolic link support in HDF5.
My reading of the bug is that it's not an issue if you use a shared library HDF5, which only works with fortran-disabled. The yt install script should be installed a non-fortran, shared hdf5. For what it's worth, I've been using HDF5 1.8.6 and h5py 1.3.1 for a while without trouble. My guess is that cc on Kraken prefers static, to the exclusion of the shared library.
-Matt
On Thu, Apr 28, 2011 at 1:12 PM, Matthew Turk matthewturk@gmail.com wrote:
For those of you not on yt-dev, here is some context on the upgrade of hdf5 to 1.8.6:
http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2011-April/001234....
On Thu, Apr 28, 2011 at 12:03 PM, Stephen Skory s@skory.us wrote:
Britton,
yes, I got the same error as you did. Some searching got me this:
https://trac.macports.org/ticket/28549
which pointed out that h5py-1.3.1 does not support hdf5-1.8.6. Does one of us want to try things with hdf5-1.8.5, or the development branch of h5py?
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (3)
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Britton Smith -
Matthew Turk -
Stephen Skory