[FLASH-USERS] flash-users Digest, Vol 45, Issue 8
Stephen Brian Amsel
samsel at umich.edu
Mon Jul 18 20:00:22 EDT 2011
Thanks!
I reinstalled HDF5, added the line you described and dealt with an
error coming from HDF5, and everything compiled. Now it just doesn't
want to run.
Following the instructions on the website, I tried "mpirun -np 3
flash4" and got
HYDU_create_process (./utils/launch/launch.c:69): execvp error on file
flash4 (No such file or directory)
three times.
Then I tried mpirun -np 3 ./flash4 and got a much nicer
./flash4: error while loading shared libraries: libhdf5.so.7: cannot
open shared object file: No such file or directory
three times.
I checked and libhdf5.so.7 is in my HDF5 library directory. Is there
an option I missed to get the program to look in the right place
during runtime?
-Stephen
Quoting John ZuHone <jzuhone at cfa.harvard.edu>:
> 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:
>>
>>> Send flash-users mailing list submissions to
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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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