[Hdf-forum] ADIOI Lock problems on NFS and Panasas

2013-04-22 Thread Mehmet Belgin
Hello everyone,

We cannot use parallel HDF5 on any of our systems. The processes either crash 
or hang (and they work with sequential HDF5). 

On NFS, we are getting:

ADIOI_Set_lock:: No locks available
ADIOI_Set_lock:offset 69744, length 256
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 124
File locking failed in ADIOI_Set_lock(fd 25,cmd F_SETLKW/7,type 
F_WRLCK/1,whence 0) with return value  and errno 25.
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).

On Panasas:

ADIOI_PANFS_RESIZE: Rank 13: Resize failed: requested=46996328 actual=9187464.

We are using intel 12.1.4, mvapich1.6 (tested with 1.8 and 1.9 as well) and 
HDF5 1.8.10. 

Is this a known problem, and do you know any workarounds without turning of the 
parallel capabilities of HDF5?

Any suggestions you may have will be appreciated!

Thanks,
-Mehmet


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Re: [Hdf-forum] HDF5 and C#

2013-04-22 Thread Charles Henderson
I am trying to run the ironpython example you sent me and I get Could not
add reference to assembly HDF5DotNet.dll.


On Thu, Apr 18, 2013 at 4:59 PM, Mitchell, Scott - IS 
scott.mitch...@exelisinc.com wrote:

  HDF5DotNet won’t run in debug mode without some tweaking. The debug
 builds of HDF add an extra ‘d’ into the name… hdf5ddll.dll, for example.
 The HDF5DotNet libraries explicitly link to the release version. So you
 need to manually change the code, the hdf dll names, or run HDF5DotNet in
 debug mode but linking to the release HDF libs. Some of these options may
 require some mods to the HDF5DotNet project as well.





 Scott



 *From:* Hdf-forum [mailto:hdf-forum-boun...@hdfgroup.org] *On Behalf Of 
 *Charles
 Henderson
 *Sent:* Thursday, April 18, 2013 4:50 PM

 *To:* HDF Users Discussion List
 *Subject:* Re: [Hdf-forum] HDF5 and C#



 okay I got IronPython for VS2010.  I am having a problem running
 HDF5DotNet in debug mode.



 I have tried everthing.  It will run without debugging.  I know there is a
 setting but can't find it.



 On Thu, Apr 18, 2013 at 9:31 AM, Charles Henderson 
 charlesshender...@gmail.com wrote:

 Well I have never seen IronPython so that will leave me in the same pickle
 that I am in with 'C'.  Is there anyway I can get some C# examples?  I need
 to know so I can tell boss whether we can do the project or not.



 On Wed, Apr 17, 2013 at 11:05 AM, Gerd Heber ghe...@hdfgroup.org wrote:

   Charles, how are you? Attached is a snippet of IronPython that does the
 job.

 I leave you the conversion to C# as an exercise. Ok?



 G.



 *From:* Hdf-forum [mailto:hdf-forum-boun...@hdfgroup.org] *On Behalf Of 
 *Charles
 Henderson
 *Sent:* Wednesday, April 17, 2013 10:44 AM
 *To:* HDF Users Discussion List
 *Subject:* [Hdf-forum] HDF5 and C#



 I am trying to convert one of the “C” examples into “C#” and not having
 much luck.



 “C” code:

 #define FILEh5ex_t_cmpdatt.h5

 #define DATASET DS1

 #define ATTRIBUTE   A1

 #define DIM04



 typedef struct {

 int serial_no;

 char*location;

 double  temperature;

 double  pressure;

 } sensor_t; /* Compound type */



 int

 main (void)

 {

 hid_t   file, filetype, memtype, strtype, space, dset, attr;

 /* Handles */

 herr_t  status;

 hsize_t dims[1] = {DIM0};

 sensor_twdata[DIM0],/* Write buffer */

 *rdata; /* Read buffer */

 int ndims,

 i;

 /* * Initialize data. */

 wdata[0].serial_no = 1153;

 wdata[0].location = Exterior (static);

 wdata[0].temperature = 53.23;

 wdata[0].pressure = 24.57;

 wdata[1].serial_no = 1184;

 wdata[1].location = Intake;

 wdata[1].temperature = 55.12;

 wdata[1].pressure = 22.95;

 wdata[2].serial_no = 1027;

 wdata[2].location = Intake manifold;

 wdata[2].temperature = 103.55;

 wdata[2].pressure = 31.23;

 wdata[3].serial_no = 1313;

 wdata[3].location = Exhaust manifold;

 wdata[3].temperature = 1252.89;

 wdata[3].pressure = 84.11;

 /* * Create a new file using the default properties. */

 file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

 /* * Create variable-length string datatype. */

 strtype = H5Tcopy (H5T_C_S1);

 status = H5Tset_size (strtype, H5T_VARIABLE);

 /* * Create the compound datatype for memory. */

 memtype = H5Tcreate (H5T_COMPOUND, sizeof (sensor_t));

 status = H5Tinsert (memtype, Serial number, HOFFSET (sensor_t,
 serial_no), H5T_NATIVE_INT);



 “C#” Code:



 string FILE = @c:\h5ex_t_cmpdatt.h5;

 string DATASET = DS1;

 string ATTRIBUTE = A1;

 int DIM0 = 4;

 int filetype, space, dset, attr, status; /* Handles */

 sensor_t[] wdata = new sensor_t[DIM0];

 int ndims, i;

 /* Initialize data. */

 wdata[0].serial_no = 1153;

 wdata[0].location = Exterior (static);

 wdata[0].temperature = 53.23;

 wdata[0].pressure = 24.57;

 wdata[1].serial_no = 1184;

 wdata[1].location = Intake;

 wdata[1].temperature = 55.12;

 wdata[1].pressure = 22.95;

 wdata[2].serial_no = 1027;

 wdata[2].location = Intake manifold;

 wdata[2].temperature = 103.55;

 wdata[2].pressure = 31.23;

 wdata[3].serial_no = 1313;

 wdata[3].location = Exhaust manifold;

 wdata[3].temperature = 1252.89;

 wdata[3].pressure = 84.11;

 /* Create a new file using the default properties. */

 H5FileId FileID = H5F.create(FILE, H5F.CreateMode.ACC_TRUNC);

 /* Create variable-length 

Re: [Hdf-forum] HDF5 1.8.11 release candidate is available for testing

2013-04-22 Thread Biddiscombe, John A.
I compiled the release candidate on win8 and win7 using VS 2012 (vs11), all 
went smoothly, comiled right out of the box (with parallel enabled and without).
I ran tests on win8 and got 2169 pass, 1 fail
Results are here.
http://cdash.hdfgroup.uiuc.edu/index.php?project=HDF518date=2013-04-22

Great job.

One thing. 

I had a discussion on the cmake list about what to do about transitive linking 
and would like to make one small change to the hdf5 cmake before the next full 
release.

If Parallel IO is enabled, any project using hdf5 also needs to pull in mpi 
includes and link to mpi lib. I'd like to add these to the hdf5-config.cmake 
when it is installed so that a project using hdf5 will pick up the mpi settings 
automatically. Currently, the user needs to add this stuff to their cmakelists 
to handle the case when mpi is used, but sometimes this can be tricky.

My use case is when paraview uses system hdf5 and it has mpi enabled, one needs 
to modify netcdf, xdmf, exodus, ... and a few other subprojects I can't 
remember to pick up the MPI settings and it is quite painful. If the 
hdf5-config added them automatically life would be much easier

Any objections?

JB


-Original Message-
From: Hdf-forum [mailto:hdf-forum-boun...@hdfgroup.org] On Behalf Of Albert 
Cheng
Sent: 12 April 2013 23:00
To: HDF Users Discussion List
Subject: [Hdf-forum] HDF5 1.8.11 release candidate is available for testing

Hello everyone,

A pre-release candidate version of HDF5 1.8.11 is available for testing and can 
be downloaded at the following link:

http://www.hdfgroup.uiuc.edu/ftp/pub/outgoing/hdf5/hdf5-1.8.11/hdf5-1.8.11-pre1.tar.gz

If you have some time to test this pre-release, we would greatly appreciate it. 
We try to test on a wide variety of platforms and environments but are unable 
to test everywhere so feedback from the user community is always welcome.

Please note that while the release notes contained in the pre-release are 
reflective of the changes and additions present in this release, the 'platforms 
tested' and 'tested configurations' sections have yet to be updated for this 
version of HDF5.

We plan to release HDF5 1.8.11 in mid-May barring the discovery of any critical 
issues.

Thank you!

The HDF Group


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Hdf-forum is for HDF software users discussion.
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Hdf-forum is for HDF software users discussion.
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