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

Alan Calder acalder at scotty.ess.sunysb.edu
Fri Jul 22 14:49:15 EDT 2011 


Put it in the Makefile.h with the c flags for HDF5:

# if we are using HDF5, we need to specify the path to the include files
CFLAGS_HDF5  = -I$(HDF5_PATH)/include -DH5_USE_16_API


On Fri, 22 Jul 2011, David Williamson wrote:

> 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>
>>
>
>

-- 

Alan C. Calder
Department of Physics and Astronomy
State University of New York at Stony Brook
Stony Brook, NY 11794-3800

email: acalder at mail.astro.sunysb.edu
office: ESS 438
phone:  (631) 632-1176
fax:  (631) 632-1745
web: http://www.astro.sunysb.edu/acalder

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