Closed dilawar closed 8 years ago
Unfortunately default hdf library installed on server is libhdf5-openmp
; which will not work without -DWITH_MPI=ON
. To bypass this, you need to point to serial version of hdf5 before you run cmake. You can set the environment variable HDF5_ROOT
to point to your version of hdf5.
HDF5_ROOT=/cluster/share/software/hdf51813 cmake ..
Re-open the ticket, if problem continues.
I see. The /cluster/share/software/hdf51813
is also compiled with openmpi support. You need to compile a version by yourself. I've put up one version in my $HOME. Try the following:
HDF5_ROOT=/home/dilawar/bin cmake ..
Hi Dilawar,
I do not have the permission to access your directory.
But I installed a version of HDF5 in my own directory and passing that to
cmake.
But when I build it (do a make) , I get the following error
libhdf5.so.10: undefined reference to SZ_BufftoBuffDecompress' libhdf5.so.10: undefined reference to
SZ_BufftoBuffCompress'
libhdf5.so.10: undefined reference to `SZ_encoder_enabled'
It seems that this might happen if the library is not linked correctly with the lhdf5 flag. I have done that too, but then it gives an error saying " cannot find -lhdf5 " Any ideas, where I may be going wrong?
Its hard to say anything without cmake/make logs.
I managed to get it working with hdf-1.8.16
source code.
Fixed the linking issue by adding the HDF5_root/lib path to rpath.
Fixed, the segfault issue with the script too. It needed a higher version of gcc than what is present on Nargis. Installed a gcc-5.2 in my local user account. And now it works!!!
On Wed, Jun 1, 2016 at 5:11 PM, Rahul Gayatri rahulgayatri84@gmail.com wrote:
Hi, sorry. Fixed the issue by adding the HDF5_root/lib path to rpath.
On Wed, Jun 1, 2016 at 5:03 PM, Dilawar Singh notifications@github.com wrote:
Please add some information what fixed the issue, even if it is trivial, when reporting on issues. Otherwise the update is useless to anyone.
On Wed, Jun 1, 2016 at 4:38 PM rahulgayatri23 notifications@github.com wrote:
HI DIlawar, Fixed the issue, some problems with the library. But still the issue of seg fault with gsolve is not solved.
On Wed, Jun 1, 2016 at 2:29 PM, Dilawar Singh <notifications@github.com
wrote:
Its hard to say anything without cmake/make logs. I managed to get it working with
hdf-1.8.16
source code.On Wed, Jun 1, 2016 at 1:03 PM, rahulgayatri23 < notifications@github.com
wrote:
Hi Dilawar, I do not have the permission to access your directory. But I installed a version of HDF5 in my own directory and passing that to cmake. But when I build it (do a make) , I get the following error libhdf5.so.10: undefined reference to
SZ_BufftoBuffDecompress' libhdf5.so.10: undefined reference to
SZ_BufftoBuffCompress' libhdf5.so.10: undefined reference to `SZ_encoder_enabled'It seems that this might happen if the library is not linked correctly with the lhdf5 flag. I have done that too, but then it gives an error saying " cannot find -lhdf5 " Any ideas, where I may be going wrong?
Regards, Rahul.
On Wed, Jun 1, 2016 at 11:28 AM, Dilawar Singh < notifications@github.com
wrote:
Reopened #126 <https://github.com/BhallaLab/moose-core/issues/126 .
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With Kind Regards G.Rahul Kumar
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Dilawar NCBS Bangalore
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With Kind Regards G.Rahul Kumar
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Dilawar
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With Kind Regards G.Rahul Kumar
With Kind Regards G.Rahul Kumar
Reported by @rahulgayatri23
On nargis, moose does not compile unless the MPI flag is set. Otherwise it gives the following error.