How much RAM do you have in the machine in question? That test is probably trying to write a 2GB or 4 GB contiguous chunk of RAM to memory so you have to have at *least* that amount installed in the system. Are you running a 32 or 64 bit system? The HDF folks will probably have a better explanation.
How much RAM do you have in the machine in question? That test is probably
trying to write a 2GB or 4 GB contiguous chunk of RAM to memory so you have
to have at *least* that amount installed in the system. Are you running a
32 or 64 bit system? The HDF folks will probably have a better explanation.
___________________________________________________________
Mike Jackson Principal Software Engineer
BlueQuartz Software Dayton, Ohio mike.jackson@bluequartz.netwww.bluequartz.net
On Dec 10, 2012, at 5:03 AM, Syed Ahsan Ali Bokhari <ahsan.pmd@gmail.com> > wrote:
>
>
>
> Dear All
>
> I am trying to install hdf-1.8.6 on RHEL5.3, I configured with the
following command
>
> ./configure --with-zlib=/usr/local/ --prefix=/usr/local/
>
> make check install fails with the following error
>
>
>
> Test passed with the Family Driver.
>
> Checking if file system supports big files...
> Testing big file with the SEC2 Driver
> Testing large dataset write
*FAILED*
> Command terminated by signal 11
> 0.02user 0.03system 0:00.06elapsed 100%CPU (0avgtext+0avgdata
0maxresident)k
> 0inputs+0outputs (0major+7343minor)pagefaults 0swaps
> make[4]: *** [big.chkexe_] Error 1
> make[4]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make[3]: *** [build-check-s] Error 2
> make[3]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make[2]: *** [test] Error 2
> make[2]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make: *** [check-recursive] Error 1
> [root@pmd03 hdf5-1.8.6]#
>
> Please help!
>
> Thanks
> Ahsan
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@hdfgroup.org
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Is your system 32 or 64-bit? What file system are you using? How much
free space do you have on the drive? Do you have any disk quotas? The
output of mount -l, df -H, and quota would be helpful.
Is the error repeatable? You don't need to re-run make check - just run
test/big directly.
make check install fails with the following error
Test passed with the Family Driver.
Checking if file system supports big files...
Testing big file with the SEC2 Driver
Testing large dataset write
*FAILED*
Command terminated by signal 11
0.02user 0.03system 0:00.06elapsed 100%CPU (0avgtext+0avgdata
0maxresident)k
0inputs+0outputs (0major+7343minor)pagefaults 0swaps
make[4]: *** [big.chkexe_] Error 1
make[4]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
make[3]: *** [build-check-s] Error 2
make[3]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
make[2]: *** [test] Error 2
make[2]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
make: *** [check-recursive] Error 1
[root@pmd03 hdf5-1.8.6]#
If it passes on the family driver and fails on SEC2, then the first thing
I'd check is that you don't have quota or disk space issues.
"With this driver, the HDF5 file’s address space is partitioned into pieces
and sent to separate storage files using an underlying driver of the user’s
choice. This driver is for systems that do not support files larger than 2
gigabytes."
···
On Mon, Dec 10, 2012 at 6:03 AM, Syed Ahsan Ali Bokhari <ahsan.pmd@gmail.com > wrote:
Dear All
I am trying to install hdf-1.8.6 on RHEL5.3, I configured with the
following command
How much RAM do you have in the machine in question? That test is probably
trying to write a 2GB or 4 GB contiguous chunk of RAM to memory so you have
to have at *least* that amount installed in the system. Are you running a
32 or 64 bit system? The HDF folks will probably have a better explanation.
___________________________________________________________
Mike Jackson Principal Software Engineer
BlueQuartz Software Dayton, Ohio mike.jackson@bluequartz.netwww.bluequartz.net
On Dec 10, 2012, at 5:03 AM, Syed Ahsan Ali Bokhari <ahsan.pmd@gmail.com> > wrote:
>
>
>
> Dear All
>
> I am trying to install hdf-1.8.6 on RHEL5.3, I configured with the
following command
>
> ./configure --with-zlib=/usr/local/ --prefix=/usr/local/
>
> make check install fails with the following error
>
>
>
> Test passed with the Family Driver.
>
> Checking if file system supports big files...
> Testing big file with the SEC2 Driver
> Testing large dataset write
*FAILED*
> Command terminated by signal 11
> 0.02user 0.03system 0:00.06elapsed 100%CPU (0avgtext+0avgdata
0maxresident)k
> 0inputs+0outputs (0major+7343minor)pagefaults 0swaps
> make[4]: *** [big.chkexe_] Error 1
> make[4]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make[3]: *** [build-check-s] Error 2
> make[3]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make[2]: *** [test] Error 2
> make[2]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make: *** [check-recursive] Error 1
> [root@pmd03 hdf5-1.8.6]#
>
> Please help!
>
> Thanks
> Ahsan
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@hdfgroup.org
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
How much RAM do you have in the machine in question? That test is
probably trying to write a 2GB or 4 GB contiguous chunk of RAM to memory so
you have to have at *least* that amount installed in the system. Are you
running a 32 or 64 bit system? The HDF folks will probably have a better
explanation.
___________________________________________________________
Mike Jackson Principal Software Engineer
BlueQuartz Software Dayton, Ohio mike.jackson@bluequartz.netwww.bluequartz.net
On Dec 10, 2012, at 5:03 AM, Syed Ahsan Ali Bokhari <ahsan.pmd@gmail.com> >> wrote:
>
>
>
> Dear All
>
> I am trying to install hdf-1.8.6 on RHEL5.3, I configured with the
following command
>
> ./configure --with-zlib=/usr/local/ --prefix=/usr/local/
>
> make check install fails with the following error
>
>
>
> Test passed with the Family Driver.
>
> Checking if file system supports big files...
> Testing big file with the SEC2 Driver
> Testing large dataset write
*FAILED*
> Command terminated by signal 11
> 0.02user 0.03system 0:00.06elapsed 100%CPU (0avgtext+0avgdata
0maxresident)k
> 0inputs+0outputs (0major+7343minor)pagefaults 0swaps
> make[4]: *** [big.chkexe_] Error 1
> make[4]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make[3]: *** [build-check-s] Error 2
> make[3]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make[2]: *** [test] Error 2
> make[2]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
> make: *** [check-recursive] Error 1
> [root@pmd03 hdf5-1.8.6]#
>
> Please help!
>
> Thanks
> Ahsan
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@hdfgroup.org
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Dear Dana the linux is 64bit. File system is ext3. There is lot of free
space on system. There is no disk quota , further output is as follows
···
*
*
*[pmdtest@pmd03 ~]$ mount -l*
/dev/mapper/KusuVolGroup00-ROOT on / type ext3 (rw)
proc on /proc type proc (rw)
sysfs on /sys type sysfs (rw)
devpts on /dev/pts type devpts (rw,gid=5,mode=620)
/dev/mapper/KusuVolGroup00-HOME on /home type ext3 (rw)
/dev/mapper/KusuVolGroup00-DEPOT on /depot type ext3 (rw)
/dev/mapper/KusuVolGroup00-VAR on /var type ext3 (rw)
/dev/sda1 on /boot type ext3 (rw) [/boot]
tmpfs on /dev/shm type tmpfs (rw)
none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
nfsd on /proc/fs/nfsd type nfsd (rw)
*[pmdtest@pmd03 ~]$ df -H*
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/KusuVolGroup00-ROOT
13G 6.6G 5.3G 56% /
/dev/mapper/KusuVolGroup00-HOME
117G 61G 51G 55% /home
/dev/mapper/KusuVolGroup00-DEPOT
11G 4.6G 5.3G 47% /depot
/dev/mapper/KusuVolGroup00-VAR
2.1G 533M 1.5G 27% /var
/dev/sda1 106M 19M 82M 19% /boot
tmpfs 4.2G 0 4.2G 0% /dev/shm
[pmdtest@pmd03 ~]$
*test/big*
Testing large dataset write
*FAILED*
HDF5-DIAG: Error detected in HDF5 (1.8.6) thread 0: #000: H5Dio.c line 266 in H5Dwrite(): can't write data
major: Dataset
minor: Write failed #001: H5Dio.c line 671 in H5D_write(): can't write data
major: Dataset
minor: Write failed #002: H5Dcontig.c line 557 in H5D_contig_write(): contiguous write failed
major: Dataset
minor: Write failed #003: H5Dselect.c line 306 in H5D_select_write(): write error
major: Dataspace
minor: Write failed #004: H5Dselect.c line 217 in H5D_select_io(): write error
major: Dataspace
minor: Write failed #005: H5Dcontig.c line 977 in H5D_contig_writevv(): block read failed
major: Low-level I/O
minor: Read failed #006: H5Fio.c line 113 in H5F_block_read(): read through metadata
accumulator failed
major: Low-level I/O
minor: Read failed #007: H5Faccum.c line 254 in H5F_accum_read(): driver read request failed
major: Low-level I/O
minor: Read failed #008: H5FDint.c line 142 in H5FD_read(): driver read request failed
major: Virtual File Layer
minor: Read failed #009: H5FDsec2.c line 745 in H5FD_sec2_read(): unable to seek to proper
position, errno = 22, error message = 'Invalid argument'
major: Low-level I/O
minor: Seek failed
*** TEST FAILED ***
Segmentation fault
Is your system 32 or 64-bit? What file system are you using? How much
free space do you have on the drive? Do you have any disk quotas? The
output of mount -l, df -H, and quota would be helpful.
Is the error repeatable? You don't need to re-run make check - just run
test/big directly.
make check install fails with the following error
Test passed with the Family Driver.
Checking if file system supports big files...
Testing big file with the SEC2 Driver
Testing large dataset write
*FAILED*
Command terminated by signal 11
0.02user 0.03system 0:00.06elapsed 100%CPU (0avgtext+0avgdata
0maxresident)k
0inputs+0outputs (0major+7343minor)pagefaults 0swaps
make[4]: *** [big.chkexe_] Error 1
make[4]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
make[3]: *** [build-check-s] Error 2
make[3]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
make[2]: *** [test] Error 2
make[2]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/home/pmdtest/hdf5-1.8.6/test'
make: *** [check-recursive] Error 1
[root@pmd03 hdf5-1.8.6]#
If it passes on the family driver and fails on SEC2, then the first thing
I'd check is that you don't have quota or disk space issues.
Finally I am able to build hdf-1.8.9 without error. But now netcdf
installation gives error looking for libhdf5_hl.so.7, I checked this
library is not present when after hdf5 is build.
How can I get this library too?
···
On Tue, Dec 11, 2012 at 11:02 PM, George N. White III <gnwiii@gmail.com>wrote:
"With this driver, the HDF5 file’s address space is partitioned into
pieces and sent to separate storage files using an underlying driver of the
user’s choice. This driver is for systems that do not support files larger
than 2 gigabytes."
On Mon, Dec 10, 2012 at 6:03 AM, Syed Ahsan Ali Bokhari < > ahsan.pmd@gmail.com> wrote:
Dear All
I am trying to install hdf-1.8.6 on RHEL5.3, I configured with the
following command
Finally I am able to build hdf-1.8.9 without error. But now netcdf
installation gives error looking for libhdf5_hl.so.7, I checked this
library is not present when after hdf5 is build.
How can I get this library too?
Since 1.8.9 works, the problem may have been due to some POSIX
incorrectness issues I fixed about that time. In POSIX read and write
calls, the number of bytes to write is unsigned and the return value (# of
bytes read/written) is signed. Writing a number of bytes greater than can
be returned via the signed value is undefined behavior. Back around 1.8.9
I changed the library to split those reads and writes into two I/O
operations.
I'm not sure why the high-level library isn't being built for you since it
should be built by default. What do you have in the target directory after
running make install? When you run configure, does it say "High Level
Library: yes" under Features?
Dana
···
On Wed, Dec 12, 2012 at 12:32 AM, Syed Ahsan Ali Bokhari < ahsan.pmd@gmail.com> wrote:
