Re: [Hdf-forum] Error building HDF5 1.8.X with Intel compilers version 14

We have confirmed there is a bug introduced in the Intel compiler, version 14, which causes the tests to fail with the option --enable-fortran2003. You can see the discussion at: http://software.intel.com/en-us/forums/topic/498698 No time frame was given for this bug being fixed by Intel,

Re: [Hdf-forum] HDF5-1.8.11 PGI link error

Thank you for the report, H5F_provisional was missing from HDF5mpi.f90, which is used when --enable-parallel is specified. The fix will be in the next release, but for now the patch is: --- HDF5mpio.f90(revision 24616) +++ HDF5mpio.f90(working copy) @@ -28,6 +28,7 @@ MODULE

[Hdf-forum] [UPDATE] RE: Error building HDF5 1.8.X with Intel compilers version 14

According to Intel, the bug fix will be in Update 2, due late January or early February. Until then, --enable-fortran2003 will not work with Intel 14. Scot From: Scot Breitenfeld Sent: Monday, January 06, 2014 12:16 PM To: hdf-forum@lists.hdfgroup.org Subject

Re: [Hdf-forum] Creating compound datatype with single dimension

Assuming you have some derived type and array: TYPE CmpField_struct INTEGER :: a REAL :: b REAL :: c ENDTYPE CmpField_struct TYPE(CmpField_struct), DIMENSION(1), TARGET :: cf You can get the offset of a, b, or c of the derived type by: offset =

Re: [Hdf-forum] VL string attribute in Fortran

I've attached a modified version of h5ex_t_vlstring_F03.f90 to use attributes instead. This example assumes you have a F2003 compiler and you used --enable-fortran2003 when you built hdf5. Hope this helps. Scot From: Hdf-forum

Re: [Hdf-forum] VL string attribute in Fortran

only for Fortran 2003? I couldn't deduce it from http://www.hdfgroup.org/HDF5/doc/RM/RM_H5A.html#Annot-Write Regards, Pierre On Wed, Feb 05, 2014 at 05:43:37PM +, Scot Breitenfeld wrote: I've attached a modified version of h5ex_t_vlstring_F03.f90 to use attributes instead. This example

Re: [Hdf-forum] compiling hdf5 gcc 4.8.1 fortran error

I could reproduce the problem you reported and we are looking into it. It works if you disable shared, --disable-shared, and build the static libraries. It also works for --enable-shared if you remove --enable-cxx, but I'm assuming you need C++ support. Scot

Re: [Hdf-forum] compiling hdf5 gcc 4.8.1 fortran error

We believe libtool is getting generated with several blank '-l''s in its postdeps variable due to mvapich's mpif90 wrapper. If you compare the output from mvapich's mpif90: mvapich2-2.0b/mvapich2/bin/mpif90 -shared -v it lists the gfortran library as -l gfortran, with a space. However, if

Re: [Hdf-forum] tH5P_F03.f90 use of SIZEOF(fill_ctype)

Hi Sean, This is on our to-do list (the fix is slated for the next release) as we have not yet incorporated any of the intrinsics from the Fortran 2008 standard. Scot On May 8, 2014, at 3:10 PM, Sean Byland se...@cray.commailto:se...@cray.com wrote: When building HDF5/1.8.13 with

Re: [Hdf-forum] Slow writing parallel HDF5 performance (for only one variable)

On Jul 10, 2014, at 6:08 PM, Angel de Vicente ang...@iac.es wrote: Hi, Angel de Vicente ang...@iac.es writes: I'm having a hard time trying to figure out what could be causing the slow I/O behaviour that I see: the same code (in Fortran) run in three different clusters behaves pretty

Re: [Hdf-forum] Slow writing parallel HDF5 performance (for only one variable)

/projects/darshan/ Scot On Jul 22, 2014, at 1:31 AM, Angel de Vicente ang...@iac.esmailto:ang...@iac.es wrote: Hi Scot, thanks for trying this out. Scot Breitenfeld brtn...@hdfgroup.orgmailto:brtn...@hdfgroup.org writes: Can you be more specific about the hardware and the software you are using

Re: [Hdf-forum] compiling hdf5 on OS/X

My bug report to gcc.gnu deals with this issue: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=48404 In summary, there is a mismatch of the LD_LIBRARY_PATH and the gcc version used to compile the code on your OS. The issue with the intel compiler is new, what is the output from the attached

Re: [Hdf-forum] compiling hdf5 on OS/X

0 0 0 0 0 0 skolio:~ dlane$ --- Dave On 28/08/2014 1:49 PM, Scot Breitenfeld wrote: My bug report to gcc.gnu deals with this issue: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=48404 In summary, there is a mismatch of the LD_LIBRARY_PATH

Re: [Hdf-forum] Gfortran: reading array of type String, length 10

Have you looked at the examples from, http://www.hdfgroup.org/HDF5/examples/api18-fortran.html namely, Read / Write String Datatype (Dataset) h5ex_t_string_F03.f90 Scot On Dec 24, 2014, at 9:46 AM, Mark Carter mcar...@markcarter.me.ukmailto:mcar...@markcarter.me.uk wrote: I'm new to HDF5

Re: [Hdf-forum] h5tset_size_f Type mismatch in argument 'size' at (1); passed INTEGER(4) to INTEGER(8)

to declare the variable in the subroutine call but it doesn't work either. Is there a specific way of doing it? Thank you On 4/2/15 17:05, Scot Breitenfeld wrote: h5tset_size is expecting an integer(size_t) in the second argument, but you are passing and integer (constant 18), instead pass INT

Re: [Hdf-forum] Issues with Intel 15 and HDF5 1.8.12

This issue will be fixed in the next release of HDF5 (the fix is already in the trunk), but for now you will have to use the Fortran compiler flag -assume nostd_value when compiling HDF5 using the Intel 15 compiler. Scot On Feb 4, 2015, at 12:18 PM, Thompson, Matt (GSFC-610.1)[SCIENCE

Re: [Hdf-forum] h5tset_size_f Type mismatch in argument 'size' at (1); passed INTEGER(4) to INTEGER(8)

h5tset_size is expecting an integer(size_t) in the second argument, but you are passing and integer (constant 18), instead pass INT(18,size_t). Scot On Feb 4, 2015, at 9:34 AM, Fabio Berzaghi f...@uw.edu wrote: Dear All, I am not able to find what throws this error when compiling this

Re: [Hdf-forum] h5tset_size_f Type mismatch in argument 'size' at (1); passed INTEGER(4) to INTEGER(8)

likely is size_t was 4 bytes on the machine you were using. Glad it works now. Scot On 4/2/15 20:15, Scot Breitenfeld wrote: The argument needs to be a scalar, so pass test(1), test(2), etc… If you have multiple calls to h5tset_size then you will have to do this in a loop, and you

Re: [Hdf-forum] fortran: 'Illegal instruction' for printing on screen the value of two variables

There are a few examples at: http://www.hdfgroup.org/HDF5/examples/api18-fortran.html which you can start from. Take a look in the “Datatypes” section, particularly at h5ex_t_floatatt_F03.f90 Scot On Mar 28, 2015, at 4:10 AM, Marco Lucchesi m.lucchesi.1...@gmail.com wrote: Dear all,

Re: [Hdf-forum] Fortran 2003 interface problem (hdf5-1.8.14)

Could you send the config.log file? What system is this for? Thanks, Scot On May 6, 2015, at 7:26 AM, Andrea Negri negri.an...@gmail.com wrote: Hi all, I have compiled the hdf5-1.8.14 library with ifort 15.0.1 20141023 and gcc 4.1.2, with the flags --enable-fortran --enable-fortran2003.

Re: [Hdf-forum] Fortran 2003 interface problem (hdf5-1.8.14)

Good point Matt, you will have to use FCFLAGS=-assume nostd_value when using intel 15 with 1.8.14. This issue has since been fixed in 1.8.15, so you will no longer need the flag. Scot On May 6, 2015, at 8:16 AM, Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]

Re: [Hdf-forum] HDF5 string read errors

You can have a look at the program h5ex_t_string_F03.f90 from: https://www.hdfgroup.org/HDF5/examples/api18-fortran.html You should be able to remove the writing section of the example and just modify the reading part in order to read your dataset. Scot On Jul 7, 2015, at 2:42 PM,

Re: [Hdf-forum] String attribute with HDF5 Lite

If you are reading a variable length string with H5LTget_attribute_string (H5T_VARIABLE) then you don’t need to allocate the string, just pass in a pointer and the library will handle the allocations. If you are reading a fixed length string then you need to allocate a string that is “large

Re: [Hdf-forum] h5dopen returns error

A few things: (1) If the integers in the dataset cannot be represented by INTEGER*4 (which I’m assuming is your native INTEGER size) then the values read from the HDF5 file will be wrong. You should be reading them into an INTEGER*8. (2) What is the most recent version of hdf you can use

Re: [Hdf-forum] h5aread_f

Can you show me how you declared your arguments in h5aread_f. Are you using any compile flags to promote any integers or reals? Thanks, Scot > On Oct 18, 2015, at 7:51 PM, Richa Mathur wrote: > > Hi > I am trying to read an attribute (N_Number_Of_Scans) that has the

Re: [Hdf-forum] h5aread_f

__ > From: Hdf-forum [hdf-forum-boun...@lists.hdfgroup.org] on behalf of Scot > Breitenfeld [brtn...@hdfgroup.org] > Sent: Monday, October 19, 2015 3:43 PM > To: HDF Users Discussion List > Subject: Re: [Hdf-forum] h5aread_f > > Can you show me how you declar

Re: [Hdf-forum] (no subject)

If you are not using h5fc to compile your code then you need to include the path to the file “hdf5.mod”. This will be found where you installed hdf5 (/opt/hdf5/include in your case). You can also look in bin/h5fc to see what include dir. you have to include, for example

Re: [Hdf-forum] h5aread_f

(0,0): 12 } Is that an array of dim(1,1) ? or a scalar? I use Integer :: ndata_dims, aread_data,error CALL h5aread_f(attr_id, H5T_NATIVE_INTEGER, aread_data,ndata_dims , error) Rgds Gompie On Mon, Oct 19, 2015 at 10:38 AM, Scot Breitenfeld <brtn...@hdfgroup.org<mailto:brtn...@h

Re: [Hdf-forum] Windows, fortran binding and tdm-gcc

Sorry for the late response, > On Sep 29, 2015, at 5:14 AM, Pascal wrote: > > Hi, > > We are trying to set up a fully open source tool chain to build our software > and are stuck on hdf5 at the moment. > When using mingw for compilation I got the error: > from >

Re: [Hdf-forum] Efficient reading of specific pixels in large HDF file

You can combine/append hyperslabs to select complex regions if that helps, see 1.4.1.1 https://www.hdfgroup.org/HDF5/doc/UG/12_Dataspaces.html, and just have one read call. Otherwise, you can use point selection, see 1.4.1.2, using one read call. In general, if the size of your hyperslabs are

Re: [Hdf-forum] There is no specific subroutine for the generic 'h5dwrite_f'

Did you also compile the HDF5 library with FCFLAGS = -fdefault-real-8 ? The problem is the native double in HDF5 does not match the native double in your program because you promoted real to double precision in your program but not in the HDF5 library. Try building the HDF5 library with

Re: [Hdf-forum] There is no specific subroutine for the generic 'h5dwrite_f'

k you for your fast answer, but I'm not an expert how to build the hdf5 library with this kind of Flag, i just made: sudo apt-get install libhdf5-serial-dev Am 03.09.2015 um 18:55 schrieb Scot Breitenfeld: Did you also compile the HDF5 library with FCFLAGS = -fdefault-real-8 ? The problem is the

Re: [Hdf-forum] H5DRead crashes on Bluegene/Q with "out of memory"

I was also getting the same error with MOAB from ANL when we were benchmarking small mesh reads with large number of processors. When I ran on 16384 processes the job would terminate with: Out of memory in file

Re: [Hdf-forum] There is no specific subroutine for the generic 'h5dwrite_f'

sudo apt-get install libhdf5-serial-dev Am 03.09.2015 um 18:55 schrieb Scot Breitenfeld: Did you also compile the HDF5 library with FCFLAGS = -fdefault-real-8 ? The problem is the native double in HDF5 does not match the native double in your program because you promoted real to double preci

Re: [Hdf-forum] Trouble building shared parallel hdf5 library on BGQ, trying to use w Darshan

Does anyone have a good (and current)recipe for building parallel hdf5 on BGQ? We are trying to encourage a community based repository of build scripts for those especially *unique* builds at: https://github.com/brtnfld/build_hdf5 You can try the “build_hdf5” script found there for the

Re: [Hdf-forum] FORTRAN and Shared Libraries

You cannot build shared libraries when enabling Fortran for 1.8 or 1.10 on the Mac using ifort or gfortran. We reported the problem to Intel at https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/543831?language=de but I’m not sure if they’ve fixed the

[Hdf-forum] Announcing release 1.1.4 of the High-level Library for handling HDF5 object and region references

A minor bug fix release of the High-level Library for handling HDF5 object and region references was released today (6/21/2016). The library contains C and Fortran APIs to: * Get information and read data pointed to by region references * Create an array of region references using paths

Re: [Hdf-forum] reading compound hdf5 data

Does the example h5ex_t_cmpd_F03.f90 at https://www.hdfgroup.org/HDF5/examples/api18-fortran.html help? > On Jun 23, 2016, at 7:41 AM, Øyvind Sylta wrote: > > Is there a simple Fortran90 instruction on reading a hdf5 dataset that uses > compound and where the dataset

Re: [Hdf-forum] reading compound hdf5 data

compiler Oyvind -Opprinnelig melding- Fra: Hdf-forum [mailto:hdf-forum-boun...@lists.hdfgroup.org] På vegne av Scot Breitenfeld Sendt: 23 June 2016 15:58 Til: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>> Emne: Re: [Hdf-forum] read

Re: [Hdf-forum] reading compound hdf5 data

hdfgroup.org] På vegne av Scot Breitenfeld Sendt: 23 June 2016 18:51 Til: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>> Emne: Re: [Hdf-forum] reading compound hdf5 data If you are using the 1.8 version of hdf5 then you have to enabl

Re: [Hdf-forum] reading compound hdf5 data

get problems. This is what confuses me. Øyvind Fra: Hdf-forum [mailto:hdf-forum-boun...@lists.hdfgroup.org] På vegne av Scot Breitenfeld Sendt: 24 June 2016 18:00 Til: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>> Emne: Re: [Hdf-forum] re

Re: [Hdf-forum] Fortran and c_int64_t

On Jan 21, 2016, at 6:55 AM, Pierre de Buyl > wrote: Hi, I am developing a Fortran code that uses HDF5. The Fortran API datatypes listed at https://www.hdfgroup.org/HDF5/doc/RM/PredefDTypes.html indicate that the Fortran

Re: [Hdf-forum] H5S_SELECT_OR_F enumeration not visible in application

Is it possible for you to try the 1.8.16 release and report back if you still have the same issue? You did call h5open_f, correct? Scot On Apr 4, 2016, at 6:41 PM, Bhamidipati, Vikram > wrote: Hello, I am static linking into

Re: [Hdf-forum] HDF5 1.10.0 Fortran H5AWRITE_F with Integers

This was fixed in the trunk, but it appears it did not make it into 1.10.0. It should be fixed in the 1.10.0 patch. Thanks, Scot > On May 12, 2016, at 7:13 PM, Matthew Clay wrote: > > Hi, > > I am transitioning to HDF5 1.10.0 to use some of the new features in the >

Re: [Hdf-forum] Building HDF for use with gcc 4.4.7 and

df5 Makefile MANIFEST test bin CMakeLists.txt config.status CTestConfig.cmake hl Makefile.am README.txt testpar Fra: Hdf-forum [mailto:hdf-forum-boun...@lists.hdfgroup.org] På vegne av Scot Breitenfeld Sendt: 21 July 2016 19:59 Til: HDF Users Discussion

Re: [Hdf-forum] Trying to read 16-bit integer from HDF5 in Fortran

On Jul 27, 2016, at 1:18 PM, Blankenship, Clay B. (MSFC-ZP11)[USRA] > wrote: Greetings...I am trying to read an HDF5 data field in Fortran which is a 16-bit integer. I have the analogous subroutines working for 4-byte reals and this

Re: [Hdf-forum] Building HDF for use with gcc 4.4.7 and

ould be fine. It is usually best to use the same compiler vendor for C and Fortran (export CC=icc, export FC=ifort) if possible. Øyvind Fra: Hdf-forum [mailto:hdf-forum-boun...@lists.hdfgroup.org] På vegne av Scot Breitenfeld Sendt: 20 July 2016 21:15 Til: HDF Users Discussion List

Re: [Hdf-forum] Fortran compiler flags for Parallel HDF5

You may have to include the path/lib to szip or zlib, and you need to link in the C HDF5 library (-lhdf5), and you may need to link in the high level HDF5 library, -lhdf5hl_fortran -lhdf5_hl Scot > On Aug 12, 2016, at 9:59 AM, Akshay Subramaniam wrote: > > Hi, > > I'm

Re: [Hdf-forum] Best Way to Patch HDF5 1.8.17 to compile with nagfor

Hi, I’ve fixed the issue in 1.8 and the fix will be in the next release of 1.8, or you can try checking out 1.8 from svn, https://svn.hdfgroup.uiuc.edu/hdf5/branches/hdf5_1_8 Also, we don’t have access to a NAG compiler, so if you can compile 1.8, run the fortran tests (i.e. in the fortran

Re: [Hdf-forum] Table vs DataSet vs PacketTable

Also, the PT/TB APIs are high-level HDF5 calls, meaning they use a series of low-level HDF5 APIs to create the PT/TB. If you are curious to see what low-level HDF5 APIs are needed, for example, to create a PT, then you can look in the HDF5 source, hl/src/H5PT.c —> H5PTcreate. Scot On Feb

Re: [Hdf-forum] Simply using the library from separate threads (C++ API)

Yes it is still the case that you cannot enable C++ or Fortran (or the High Level APIs) when threadsafe is enabled. —enable-unsupported can override this behavior. Scot > On Sep 22, 2016, at 12:36 PM, Elvis Stansvik > wrote: > > 2016-09-22 19:23 GMT+02:00

Re: [Hdf-forum] Best Way to Patch HDF5 1.8.17 to compile with nagfor

> On Aug 23, 2016, at 10:42 AM, Schluenzen, Frank <frank.schluen...@desy.de> > wrote: > > Hi, > > - Original Message - >> From: "Scot Breitenfeld" <brtn...@hdfgroup.org> >> To: "HDF Users Discussion List" <hdf-forum@lists.hdfgr

Re: [Hdf-forum] Writing File Fails on Windows 10 with Intel Fortran 17 with HDF5 1.8.15

How far in the program does it get before it segfaults? Can you post the output from the program? I tried a sample program on Windows 10, Intel 17, and HDF5 1.8.17, but I’m having issues with the HDF5 Fortran parameters not getting set when building the program inside Visual Studio. Can you

Re: [Hdf-forum] CMake 3.7.x incompatible?

We have noticed this behavior in the past. I tried on my macOS 10.12.x, with 1_8, 1.8.18 and develop and did not have any problems. I tried gfortran 6.3.0 with both gcc 6.3 and the system's gcc, but I have cmake 3.8.0. From your previous email, it looks like cmake failed in detecting the

Re: [Hdf-forum] Reading character string attribute in Fortran

Hi, Take a look at the examples in the “Datatypes” section at: https://support.hdfgroup.org/HDF5/examples/api-fortran.html namely (for fixed sized string), h5ex_t_stringCatt_F03.f90. Scot > On May 16, 2017, at 9:55 AM, Greenberg, Naomi > wrote: > > I am

Re: [Hdf-forum] HDF5 library hang in H5DWrite_f in collective mode

denes >> On 05/20/2017 09:12 PM, Quincey Koziol wrote: >>> >>>> On May 19, 2017, at 12:32 PM, Håkon Strandenes <haa...@hakostra.net> wrote: >>>> >>>> Yes, the issue is still there. >>>> >>>> I will try to make a dummy

Re: [Hdf-forum] HDF5 library hang in H5DWrite_f in collective mode

Can you try it with 1.10.1 and see if you still have an issue. Scot > On May 19, 2017, at 1:11 PM, Quincey Koziol wrote: > > Hi Håkon, > >> On May 19, 2017, at 10:01 AM, Håkon Strandenes wrote: >> >> (sorry, forgot to cc mailing list in prev. mail) >>

Re: [Hdf-forum] HDF5 object oriented Fortran Library

Hi Ricardo, I just did a quick glance, and I noticed a few things. (1) Have you considered passing the C address of the array arguments instead to your functions? That would simplify your interfaces and remove a lot of code duplication. Also, using the F2003 HDF5 functions instead would also

Re: [Hdf-forum] Errors when install HDF5

Did you patch the Fortran source for Intel 18? https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951 Scot On Nov 30, 2017, at 8:13 AM, 江捷 > wrote: Hello Barbara, Thank you for your reply.

Re: [Hdf-forum] [Build] Unable to access module symbol file for module h5fortran_types

Thanks for the report Robert, We’ve reproduced the issue, and it's slated to be fixed in the next release of HDF5 1.10. Scot > On Dec 9, 2017, at 3:38 AM, Robert Sawko wrote: > > Dear HDFers, > > I am building a parallel version of HDF5 sub-version 1.10.1. I went with the

Re: [Hdf-forum] Hdf-forum Digest, Vol 101, Issue 5

lists.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. Memory allocation/deallocation (Andreas Derler) 2. Re: no specif

Re: [Hdf-forum] [SPAM] Errors when install HDF5

target 'check-am' failed make[1]: *** [check-am] Error 2 make[1]: Leaving directory '/home/ustc/下载/hdf5-1.10.1/testpar' Makefile:650: recipe for target 'check-recursive' failed make: *** [check-recursive] Error 1" I have attached the configure.out, make.out, check.out and config.log. Bests Reg

Re: [Hdf-forum] Comping with enable-parallel, gfortran error

Can you send the config.log file, it should contain the details of the error. Scot On Jan 26, 2018, at 3:57 PM, Paul Arias > wrote: Hello, I am trying to compile HDF5 (1.8.20) with openmpi, fortran (gnu). This is the error message that I

Re: [Hdf-forum] New member : HDF5 previous to Finite Element Analyses

If you are looking for an FEA “standard” I/O format, it does not exist. CGNS is as close as it gets, but that is for CFD data. There has been some discussion in the past to extend CGNS to include Solid Mechanics, but it never gained traction. For FEA data formats which are geared towards solid