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

Sun Jul 17 16:51:50 EDT 2011

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>