[FLASH-USERS] flash-users Digest, Vol 45, Issue 8

David Williamson david.john.williamson at gmail.com
Fri Jul 22 14:42:25 EDT 2011 

Hi all,

Coincidentally, I'm getting this exact error as well.

Where should I add -DH5_USE_16_API in the hdf5 compilation? Do I just add it to the ./configure option, or do I have to do some manual tweaking of the Makefile?

Cheers,
-Dave

On 17/07/2011, at 5:51 PM, John ZuHone wrote:

> Hi Stephen,
> 
> I checked my HDF5 (1.8.5) install on my laptop and noticed the following headers in the include subdirectory:
> 
> H5ACpublic.h  H5Epublic.h   H5FDmpiposix.h  H5IMpublic.h  H5Ppublic.h   H5Tpublic.h
> H5api_adpt.h  H5FDcore.h    H5FDmulti.h     H5Ipublic.h   H5PTpublic.h  H5version.h
> H5Apublic.h   H5FDdirect.h  H5FDpublic.h    H5Lpublic.h   H5pubconf.h   H5Zpublic.h
> H5Cpublic.h   H5FDfamily.h  H5FDsec2.h      H5LTpublic.h  H5public.h    hdf5.h
> H5Dpublic.h   H5FDlog.h     H5FDstdio.h     H5MMpublic.h  H5Rpublic.h   hdf5_hl.h
> H5DSpublic.h  H5FDmpi.h     H5Fpublic.h     H5Opublic.h   H5Spublic.h
> H5Epubgen.h   H5FDmpio.h    H5Gpublic.h     H5overflow.h  H5TBpublic.h
> 
> I also find this line a little curious:
> 
> LIB_HDF5 = -L $(HDF5_PATH)/lib -L $(HDF5_PATH)/lib64 -lhdf5 -lz
> 
> Why are you linking from both the lib and lib64 directories? Are you building a 32 or 64-bit executable? 
> 
> By the way, can you figure out what version they installed? FLASH uses the API from the 1.6.* series of HDF5, whereas that has changed for the current series, which is 1.8.*. If the sysadmins installed 1.8.*, then you need to add this to the compile line: 
> 
> -DH5_USE_16_API
> 
> Just a few things to check. 
> 
> Best,
> 
> John
> 
> On Jul 17, 2011, at 4:35 PM, Stephen Brian Amsel wrote:
> 
>> I've attached the Makefile.h. It's almost identical to the Intel prototype Makefile.h under Linux.
>> 
>> I got HDF5 installed on my computer through tech support in my department because at the time I didn't have administrative privileges on my computer. (I've been trying to install FLASH on my desktop so that I could learn how to use it properly without tying up the cluster's head node waiting through the its queue as I try each different thing.) I don't know whether they just got the binary or downloaded the library's source without the headers.
>> 
>> Quoting flash-users-request at flash.uchicago.edu:
>> 
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>>> Today's Topics:
>>> 
>>>  1.  trouble compiling flash with hdf5 (Stephen Brian Amsel)
>>>  2. Re:  trouble compiling flash with hdf5 (John ZuHone)
>>> 
>>> 
>>> ----------------------------------------------------------------------
>>> 
>>> Message: 1
>>> Date: Sat, 16 Jul 2011 20:41:01 -0400
>>> From: Stephen Brian Amsel <samsel at umich.edu>
>>> Subject: [FLASH-USERS] trouble compiling flash with hdf5
>>> To: flash-users at flash.uchicago.edu
>>> Message-ID: <20110716204101.10975dd2j5f79400 at web.mail.umich.edu>
>>> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
>>> 	format="flowed"
>>> 
>>> Hi,
>>> 
>>> I'm trying to install FLASH4 (alpha) on machine with a Red Hat OS and
>>> an Intel processor using the Intel compiler. (I could not find the
>>> architecture of the Dell Optiplex GX620 if that matters.) A problem
>>> arises in io_h5_type.h. The include-command for hdf5.h works, but not
>>> the commands which use hid_t, which is used in hdf5.h. I get:
>>> io_h5_type.h(10): error: identifier "hid_t" is undefined
>>>  hid_t io_h5_type_hid_primitive(const int flashType);
>>> 
>>> and the same for lines 11-13.
>>> 
>>> When I got HDF5, I did not get all the headers. I found and downloaded
>>> the HDF5 header, but if there are any others specific to HDF5 that I
>>> need, I don't have them. I don't know if that is an issue as hid_t is
>>> used in HDF5 and that did not produce an error either here or in a
>>> test-program which included it. (The test-program compiled when it
>>> called nothing but a printf to say it ran successfully, but ran into
>>> an error when I tried to use hid_t.)
>>> 
>>> -Stephen
>>> 
>>> 
>>> ------------------------------
>>> 
>>> Message: 2
>>> Date: Sun, 17 Jul 2011 00:25:47 -0400
>>> From: John ZuHone <jzuhone at cfa.harvard.edu>
>>> Subject: Re: [FLASH-USERS] trouble compiling flash with hdf5
>>> To: Stephen Brian Amsel <samsel at umich.edu>
>>> Cc: flash-users at flash.uchicago.edu
>>> Message-ID: <C742315D-640C-4D09-9AE3-E6C9EFE1ED5D at cfa.harvard.edu>
>>> Content-Type: text/plain; charset=us-ascii
>>> 
>>> Hi Stephen,
>>> 
>>> A couple of things that may be helpful to us as we try to debug your problem:
>>> 
>>> 1) Can you send us your Makefile.h? It is the Makefile definitions file that is specific to your machine, which you should have probably custom-edited from a similar one in FLASH4/sites.
>>> 
>>> 2) Could you explain a bit more how you got HDF5? Did you download the source from the website and compile and install it, or did you have some sort of binary package?
>>> 
>>> Best,
>>> 
>>> John ZuHone
>>> 
>>> On Jul 16, 2011, at 8:41 PM, Stephen Brian Amsel wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I'm trying to install FLASH4 (alpha) on machine with a Red Hat OS and an Intel processor using the Intel compiler. (I could not find the architecture of the Dell Optiplex GX620 if that matters.) A problem arises in io_h5_type.h. The include-command for hdf5.h works, but not the commands which use hid_t, which is used in hdf5.h. I get:
>>>> io_h5_type.h(10): error: identifier "hid_t" is undefined
>>>> hid_t io_h5_type_hid_primitive(const int flashType);
>>>> 
>>>> and the same for lines 11-13.
>>>> 
>>>> When I got HDF5, I did not get all the headers. I found and downloaded the HDF5 header, but if there are any others specific to HDF5 that I need, I don't have them. I don't know if that is an issue as hid_t is used in HDF5 and that did not produce an error either here or in a test-program which included it. (The test-program compiled when it called nothing but a printf to say it ran successfully, but ran into an error when I tried to use hid_t.)
>>>> 
>>>> -Stephen
>>> 
>>> 
>>> 
>>> ------------------------------
>>> 
>>> _______________________________________________
>>> flash-users mailing list
>>> flash-users at flash.uchicago.edu
>>> http://flash.uchicago.edu/mailman/listinfo/flash-users
>>> 
>>> 
>>> End of flash-users Digest, Vol 45, Issue 8
>>> ******************************************
>>> 
>>> 
>>> 
>> 
>> 
>> <Makefile.h>
>

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