Re: Error when doing make

From: Dimitry Ayzenberg <dayzenbe_at_andrew.cmu.edu>
Date: Thu, 10 Sep 2009 23:14:35 -0400

Should the makefile be like this:

ifeq ($(SYSTYPE),"mine")
CC = mpicc
OPTIMIZE = -O3 -Wall
GSL_INCL = -I/usr/local/include
GSL_LIBS = -L/usr/local/lib
FFTW_INCL= -I/usr/local/include
FFTW_LIBS= -L/usr/local/lib
MPICHLIB = -L/usr/local/lib
HDF5INCL = -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include
HDF5LIB = -L/home/dimitry/Desktop/hdf5-1.6.9/hdf5/lib -lhdf5 -static
endif

Because when I do that I get the following error when I run make:

/usr/local/lib/libmpich.a(simple_pmi.o): In function `PMI_Init':
simple_pmi.c:(.text+0x267b): warning: Using 'gethostbyname' in statically
linked applications requires at runtime the shared libraries from the
glibc version used for linking
/usr/local/lib/libsfftw.a(rader.o): In function `fftw_make_node_rader':
rader.c:(.text+0xfcd): undefined reference to `sincos'
/usr/local/lib/libsfftw.a(twiddle.o): In function `fftw_create_twiddle':
twiddle.c:(.text+0x249): undefined reference to `sincos'
twiddle.c:(.text+0x37e): undefined reference to `sincos'
twiddle.c:(.text+0x454): undefined reference to `sincos'
collect2: ld returned 1 exit status
make: *** [Gadget2] Error 1

Dimitry


On Thu, September 10, 2009 22:39, SangHoon Oh wrote:
> Hi,
>
>
> If dynamic link doesn't work, please try static library link.
> Add -static to CFLAGS.
>
>
> Good luck,
>
>
> SangHoon
>
>
> On Fri, Sep 11, 2009 at 11:27 AM, Dimitry Ayzenberg
> <dayzenbe_at_andrew.cmu.edu> wrote:
>
>>
>> Still having the same issue. I tried a few different things to fix it
>> but nothing worked. Can anyone please help?
>>
>> Dimitry
>>
>>
>>
>> On Wed, September 9, 2009 23:58, Dimitry Ayzenberg wrote:
>>
>>>
>>
>>> Like this:
>>>
>>>
>>>
>>> export
>>> LD_LIBRARY_PATH=/home/dimitry/Desktop/hdf5-1.6.9/hdf5/lib:$LD_LIBRARY
>>> _PAT
>>> H
>>>
>>>
>>>
>>> Is there supposed to be some output when I do that?
>>> It still comes up with the same error even when I do that? Does it
>>> matter what folder I'm in when I run the export command?
>>>
>>> Dimitry
>>>
>>>
>>>
>>>
>>> On Wed, September 9, 2009 23:43, Scott Wales wrote:
>>>
>>>
>>>> You need to add the directory with libhdf5.so.0 to the environment
>>>> variable LD_LIBRARY_PATH. In bash, use export
>>>> LD_LIBRARY_PATH=/path/to/hdf5/lib:$LD_LIBRARY_PATH then try running
>>>> gadget. Other shells may have different ways to set variables.
>>>>
>>>> LD_LIBRARY_PATH tells the dynamic linker where to look for shared
>>>> libraries.
>>>>
>>>> Cheers, Scott.
>>>>
>>>>
>>>>
>>>>
>>>> On 10/09/2009, at 12:57 PM, Dimitry Ayzenberg wrote:
>>>>
>>>>
>>>>
>>>>
>>>>>
>>>>> Yeah I just forgot to add -lhdf5 to the makefile after the
>>>>> location for the hdf5 include file. It finally finished making.
>>>>> But now I have
>>>>> an issue when I try one of the example param files. I get the
>>>>> error:
>>>>>
>>>>>
>>>>> error while loading shared libraries: libhdf5.so.0: cannot open
>>>>> shared object file: No such file or directory.
>>>>>
>>>>> But the file does exist and it's where it should be. Anyone know
>>>>> why that's happening?
>>>>>
>>>>> Dimitry
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Wed, September 9, 2009 22:49, Scott Wales wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hi Dimitry,
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> This looks like a linker error. Make sure you're linking to the
>>>>>> correct HDF5 libraries. It will probably compile fine if you
>>>>>> turn off HDF5 support.
>>>>>>
>>>>>> Cheers, Scott Wales
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 10/09/2009, at 12:35 PM, Dimitry Ayzenberg wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> After a quick google search I fixed that issue. Now I have
>>>>>>> one that's much odder. I'll just paste the part of the make
>>>>>>> output where it goes wrong.
>>>>>>>
>>>>>>> io.o: In function `write_header_attributes_in_hdf5':
>>>>>>> io.c:(.text+0x4d2): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x4f3): undefined reference to
>>>>>>> `H5Sset_extent_simple'
>>>>>>> io.c:(.text+0x4f8): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x4fd): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0x51d): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x524): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x529): undefined reference to `H5T_NATIVE_UINT_g'
>>>>>>> io.c:(.text+0x53d): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0x545): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0x54d): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x559): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x57a): undefined reference to
>>>>>>> `H5Sset_extent_simple'
>>>>>>> io.c:(.text+0x57f): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x584): undefined reference to `H5T_NATIVE_UINT_g'
>>>>>>> io.c:(.text+0x5a4): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x5ab): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x5b0): undefined reference to `H5T_NATIVE_UINT_g'
>>>>>>> io.c:(.text+0x5c4): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0x5cc): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0x5d4): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x5e0): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x601): undefined reference to
>>>>>>> `H5Sset_extent_simple'
>>>>>>> io.c:(.text+0x606): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x60b): undefined reference to `H5T_NATIVE_UINT_g'
>>>>>>> io.c:(.text+0x62b): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x632): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x637): undefined reference to `H5T_NATIVE_UINT_g'
>>>>>>> io.c:(.text+0x64b): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0x653): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0x65b): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x667): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x688): undefined reference to
>>>>>>> `H5Sset_extent_simple'
>>>>>>> io.c:(.text+0x68d): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x692): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x6b2): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x6b9): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x6be): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x6d2): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0x6da): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0x6e2): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x6ee): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x6f5): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x6fa): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x71a): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x721): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x726): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x73a): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0x742): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0x74a): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x756): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x75d): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x762): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x782): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x789): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x78e): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x7a2): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0x7aa): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0x7b2): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x7be): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x7c5): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x7ca): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x7ea): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x7f1): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x7f6): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x80a): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0x812): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0x81a): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x826): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x82d): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x832): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0x852): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x859): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x85e): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0x872): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0x87a): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0x882): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x88e): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x895): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x89a): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x8ba): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x8c1): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x8c6): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x8da): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0x8e2): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0x8ea): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x8f6): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x8fd): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x902): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x922): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x929): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x92e): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x942): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0x94a): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0x952): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x95e): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x965): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x96a): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x98a): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x991): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x996): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> io.c:(.text+0x9aa): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0x9b2): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0x9ba): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x9c6): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0x9cd): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x9d2): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0x9f2): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0x9f9): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x9fe): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0xa12): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0xa1a): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0xa22): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0xa2e): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0xa35): undefined reference to `H5open'
>>>>>>> io.c:(.text+0xa3a): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0xa5a): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0xa61): undefined reference to `H5open'
>>>>>>> io.c:(.text+0xa66): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0xa7a): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0xa82): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0xa8a): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0xa96): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0xa9d): undefined reference to `H5open'
>>>>>>> io.c:(.text+0xaa2): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0xac2): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0xac9): undefined reference to `H5open'
>>>>>>> io.c:(.text+0xace): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0xae2): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0xaea): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0xaf2): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0xafe): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0xb05): undefined reference to `H5open'
>>>>>>> io.c:(.text+0xb0a): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0xb2a): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0xb31): undefined reference to `H5open'
>>>>>>> io.c:(.text+0xb36): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0xb4a): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0xb52): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0xb5a): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0xb66): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0xb6d): undefined reference to `H5open'
>>>>>>> io.c:(.text+0xb72): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0xb92): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0xb99): undefined reference to `H5open'
>>>>>>> io.c:(.text+0xb9e): undefined reference to `H5T_NATIVE_INT_g'
>>>>>>> io.c:(.text+0xbb2): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0xbba): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0xbc2): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0xbd8): undefined reference to `H5Screate'
>>>>>>> io.c:(.text+0xbf9): undefined reference to
>>>>>>> `H5Sset_extent_simple'
>>>>>>> io.c:(.text+0xbfe): undefined reference to `H5open'
>>>>>>> io.c:(.text+0xc03): undefined reference to `H5T_NATIVE_UINT_g'
>>>>>>> io.c:(.text+0xc23): undefined reference to `H5Acreate'
>>>>>>> io.c:(.text+0xc2a): undefined reference to `H5open'
>>>>>>> io.c:(.text+0xc2f): undefined reference to `H5T_NATIVE_UINT_g'
>>>>>>> io.c:(.text+0xc43): undefined reference to `H5Awrite'
>>>>>>> io.c:(.text+0xc4b): undefined reference to `H5Aclose'
>>>>>>> io.c:(.text+0xc53): undefined reference to `H5Sclose'
>>>>>>> io.o: In function `write_file':
>>>>>>> io.c:(.text+0x1d1f): undefined reference to
>>>>>>> `H5Sselect_hyperslab'
>>>>>>> io.c:(.text+0x1d7a): undefined reference to `H5Screate_simple'
>>>>>>> io.c:(.text+0x1db3): undefined reference to `H5Dwrite'
>>>>>>> io.c:(.text+0x1dbb): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x20dd): undefined reference to `H5Dclose'
>>>>>>> io.c:(.text+0x20eb): undefined reference to `H5Sclose'
>>>>>>> io.c:(.text+0x20f9): undefined reference to `H5Tclose'
>>>>>>> io.c:(.text+0x212c): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x2131): undefined reference to
>>>>>>> `H5T_NATIVE_FLOAT_g'
>>>>>>> io.c:(.text+0x2139): undefined reference to `H5Tcopy'
>>>>>>> io.c:(.text+0x21df): undefined reference to `H5Screate_simple'
>>>>>>> io.c:(.text+0x2214): undefined reference to `H5Dcreate'
>>>>>>> io.c:(.text+0x25e0): undefined reference to `H5open'
>>>>>>> io.c:(.text+0x25e5): undefined reference to
>>>>>>> `H5T_NATIVE_UINT_g'
>>>>>>> io.c:(.text+0x25ed): undefined reference to `H5Tcopy'
>>>>>>> io.c:(.text+0x2655): undefined reference to `H5Gclose'
>>>>>>> io.c:(.text+0x266b): undefined reference to `H5Gclose'
>>>>>>> io.c:(.text+0x2679): undefined reference to `H5Fclose'
>>>>>>> io.c:(.text+0x26d2): undefined reference to `H5check_version'
>>>>>>> io.c:(.text+0x26f2): undefined reference to `H5Fcreate'
>>>>>>> io.c:(.text+0x2710): undefined reference to `H5Gcreate'
>>>>>>> io.c:(.text+0x275f): undefined reference to `H5Gcreate'
>>>>>>> read_ic.o: In function `read_header_attributes_in_hdf5':
>>>>>>> read_ic.c:(.text+0x1e4): undefined reference to
>>>>>>> `H5check_version'
>>>>>>> read_ic.c:(.text+0x1fc): undefined reference to `H5Fopen'
>>>>>>> read_ic.c:(.text+0x20e): undefined reference to `H5Gopen'
>>>>>>> read_ic.c:(.text+0x220): undefined reference to `H5Aopen_name'
>>>>>>> read_ic.c:(.text+0x227): undefined reference to `H5open'
>>>>>>> read_ic.c:(.text+0x22c): undefined reference to
>>>>>>> `H5T_NATIVE_INT_g'
>>>>>>>  read_ic.c:(.text+0x240): undefined reference to `H5Aread'
>>>>>>> read_ic.c:(.text+0x248): undefined reference to `H5Aclose'
>>>>>>> read_ic.c:(.text+0x258): undefined reference to `H5Aopen_name'
>>>>>>> read_ic.c:(.text+0x25f): undefined reference to `H5open'
>>>>>>> read_ic.c:(.text+0x264): undefined reference to
>>>>>>> `H5T_NATIVE_UINT_g'
>>>>>>> read_ic.c:(.text+0x278): undefined reference to `H5Aread'
>>>>>>> read_ic.c:(.text+0x280): undefined reference to `H5Aclose'
>>>>>>> read_ic.c:(.text+0x290): undefined reference to `H5Aopen_name'
>>>>>>> read_ic.c:(.text+0x297): undefined reference to `H5open'
>>>>>>> read_ic.c:(.text+0x29c): undefined reference to
>>>>>>> `H5T_NATIVE_UINT_g'
>>>>>>> read_ic.c:(.text+0x2b0): undefined reference to `H5Aread'
>>>>>>> read_ic.c:(.text+0x2b8): undefined reference to `H5Aclose'
>>>>>>> read_ic.c:(.text+0x2c8): undefined reference to `H5Aopen_name'
>>>>>>> read_ic.c:(.text+0x2cf): undefined reference to `H5open'
>>>>>>> read_ic.c:(.text+0x2d4): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> read_ic.c:(.text+0x2e8): undefined reference to `H5Aread'
>>>>>>> read_ic.c:(.text+0x2f0): undefined reference to `H5Aclose'
>>>>>>> read_ic.c:(.text+0x300): undefined reference to `H5Aopen_name'
>>>>>>> read_ic.c:(.text+0x307): undefined reference to `H5open'
>>>>>>> read_ic.c:(.text+0x30c): undefined reference to
>>>>>>> `H5T_NATIVE_DOUBLE_g'
>>>>>>> read_ic.c:(.text+0x320): undefined reference to `H5Aread'
>>>>>>> read_ic.c:(.text+0x328): undefined reference to `H5Aclose'
>>>>>>> read_ic.c:(.text+0x338): undefined reference to `H5Aopen_name'
>>>>>>> read_ic.c:(.text+0x33f): undefined reference to `H5open'
>>>>>>> read_ic.c:(.text+0x344): undefined reference to
>>>>>>> `H5T_NATIVE_INT_g'
>>>>>>>  read_ic.c:(.text+0x358): undefined reference to `H5Aread'
>>>>>>> read_ic.c:(.text+0x360): undefined reference to `H5Aclose'
>>>>>>> read_ic.c:(.text+0x370): undefined reference to `H5Aopen_name'
>>>>>>> read_ic.c:(.text+0x377): undefined reference to `H5open'
>>>>>>> read_ic.c:(.text+0x37c): undefined reference to
>>>>>>> `H5T_NATIVE_INT_g'
>>>>>>>  read_ic.c:(.text+0x390): undefined reference to `H5Aread'
>>>>>>> read_ic.c:(.text+0x398): undefined reference to `H5Aclose'
>>>>>>> read_ic.c:(.text+0x3a0): undefined reference to `H5Gclose'
>>>>>>> read_ic.o: In function `read_file':
>>>>>>> read_ic.c:(.text+0x128b): undefined reference to `H5Dopen'
>>>>>>> read_ic.c:(.text+0x12f7): undefined reference to
>>>>>>> `H5Screate_simple'
>>>>>>> read_ic.c:(.text+0x1340): undefined reference to
>>>>>>> `H5Screate_simple'
>>>>>>> read_ic.c:(.text+0x13de): undefined reference to
>>>>>>> `H5Sselect_hyperslab'
>>>>>>> read_ic.c:(.text+0x1411): undefined reference to `H5open'
>>>>>>> read_ic.c:(.text+0x1416): undefined reference to
>>>>>>> `H5T_NATIVE_UINT_g'
>>>>>>> read_ic.c:(.text+0x141e): undefined reference to `H5Tcopy'
>>>>>>> read_ic.c:(.text+0x1461): undefined reference to `H5Dread'
>>>>>>> read_ic.c:(.text+0x146f): undefined reference to `H5Tclose'
>>>>>>> read_ic.c:(.text+0x1477): undefined reference to `H5Sclose'
>>>>>>> read_ic.c:(.text+0x1485): undefined reference to `H5Sclose'
>>>>>>> read_ic.c:(.text+0x1493): undefined reference to `H5Dclose'
>>>>>>> read_ic.c:(.text+0x1541): undefined reference to `H5open'
>>>>>>> read_ic.c:(.text+0x1546): undefined reference to
>>>>>>> `H5T_NATIVE_UINT64_g'
>>>>>>> read_ic.c:(.text+0x154e): undefined reference to `H5Tcopy'
>>>>>>> read_ic.c:(.text+0x1561): undefined reference to `H5open'
>>>>>>> read_ic.c:(.text+0x1566): undefined reference to
>>>>>>> `H5T_NATIVE_FLOAT_g'
>>>>>>> read_ic.c:(.text+0x156e): undefined reference to `H5Tcopy'
>>>>>>> read_ic.c:(.text+0x173d): undefined reference to `H5Gclose'
>>>>>>> read_ic.c:(.text+0x1754): undefined reference to `H5Gclose'
>>>>>>> read_ic.c:(.text+0x176b): undefined reference to `H5Gclose'
>>>>>>> read_ic.c:(.text+0x1783): undefined reference to `H5Gclose'
>>>>>>> read_ic.c:(.text+0x179b): undefined reference to `H5Gclose'
>>>>>>> read_ic.o:read_ic.c:(.text+0x17b3): more undefined references
>>>>>>> to `H5Gclose' follow
>>>>>>> read_ic.o: In function `read_file':
>>>>>>> read_ic.c:(.text+0x17c1): undefined reference to `H5Fclose'
>>>>>>> read_ic.c:(.text+0x1a65): undefined reference to
>>>>>>> `H5check_version'
>>>>>>>  read_ic.c:(.text+0x1a83): undefined reference to `H5Fopen'
>>>>>>> read_ic.c:(.text+0x1ad2): undefined reference to `H5Gopen'
>>>>>>> read_ic.c:(.text+0x1b22): undefined reference to `H5Gopen'
>>>>>>> read_ic.c:(.text+0x1b72): undefined reference to `H5Gopen'
>>>>>>> read_ic.c:(.text+0x1bc2): undefined reference to `H5Gopen'
>>>>>>> read_ic.c:(.text+0x1c12): undefined reference to `H5Gopen'
>>>>>>> read_ic.o:read_ic.c:(.text+0x1c66): more undefined references
>>>>>>> to `H5Gopen'
>>>>>>> follow read_ic.o: In function
>>>>>>> `read_header_attributes_in_hdf5':
>>>>>>> read_ic.c:(.text+0x3af): undefined reference to `H5Fclose'
>>>>>>> collect2: ld returned 1 exit status
>>>>>>> make: *** [Gadget2] Error 1
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dimitry
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Wed, September 9, 2009 22:07, Dimitry Ayzenberg wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> No that didn't fix it. Same error. Seems like it can't find
>>>>>>>> srfftw_mpi.h. What would that not being there be caused
>>>>>>>> by? The fftw install or the mpi install?
>>>>>>>>
>>>>>>>> Dimitry
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, September 9, 2009 21:40, Dimitry Ayzenberg wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>> I figured out the problem, I think. I used version 3 of
>>>>>>>>> fftw which apparently doesn't work. Retrying with version
>>>>>>>>> 2 and
>>>>>>>>> using the extra configuration options that are shown in
>>>>>>>>> the guide.
>>>>>>>>>
>>>>>>>>> Dimitry
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, September 9, 2009 21:35, Dimitry Ayzenberg wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> No I'm pretty sure those are properly set, especially
>>>>>>>>>> since  make got past the part where it checks if all
>>>>>>>>>> the headers are available.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Dimitry
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wed, September 9, 2009 20:58, SangHoon Oh wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Perhaps you didn't include the FFTW headers properly.
>>>>>>>>>>> Please check the CFLAGS whether
>>>>>>>>>>> -I/PATH/TO/FFTW/HEADERS
>>>>>>>>>>> is set to correct the path.
>>>>>>>>>>>
>>>>>>>>>>> Good luck,
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> SangHoon
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Thu, Sep 10, 2009 at 8:09 AM, Dimitry
>>>>>>>>>>> Ayzenberg<dayzenbe_at_andrew.cmu.edu> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Okay so that worked after I switched to version
>>>>>>>>>>>> 1.6.9
>>>>>>>>>>>> and that error didn't come up again. But now this
>>>>>>>>>>>> comes up:
>>>>>>>>>>>> (sorry
>>>>>>>>>>>> that I pasted all of it but I figure that would help
>>>>>>>>>>>> whoever helps me figure it out easier)
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> dimitry_at_Phoenix:~/Desktop/Gadget-2.0.4/Gadget2$
>>>>>>>>>>>> sudo make mpicc ‚  ‚ -O3 -Wall -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  main.o main.c mpicc ‚  ‚ -O3 -Wall -DPERIODIC
>>>>>>>>>>>> ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  run.o run.c run.c: In function â‚œrunâ‚„:
>>>>>>>>>>>> run.c:102:
>>>>>>>>>>>> warning:
>>>>>>>>>>>> ignoring return value of â‚œsystemâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result mpicc ‚
>>>>>>>>>>>>  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC
>>>>>>>>>>>> ‚ -DUNEQUALSOFTENINGS -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  predict.o predict.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  begrun.o begrun.c begrun.c: In function
>>>>>>>>>>>> â‚œread_parameter_fileâ‚„:
>>>>>>>>>>>> begrun.c:602:
>>>>>>>>>>>> warning: ignoring return value of
>>>>>>>>>>>> â‚œfgetsâ‚„, declared
>>>>>>>>>>>> with attribute warn_unused_result begrun.c:653:
>>>>>>>>>>>> warning:
>>>>>>>>>>>>  ignoring return value of â‚œsystemâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result mpicc ‚
>>>>>>>>>>>>  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  endrun.o endrun.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  global.o global.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  timestep.o timestep.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC
>>>>>>>>>>>> ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  init.o init.c mpicc ‚  ‚ -O3 -Wall -DPERIODIC
>>>>>>>>>>>> ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  restart.o restart.c restart.c: In function
>>>>>>>>>>>> â‚œrestartâ‚„:
>>>>>>>>>>>> restart.c:78:
>>>>>>>>>>>> warning:
>>>>>>>>>>>> ignoring return value of â‚œsystemâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result mpicc ‚
>>>>>>>>>>>>  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  io.o io.c io.c: In function
>>>>>>>>>>>> â‚œwrite_fileâ‚„:
>>>>>>>>>>>> io.c:687:
>>>>>>>>>>>> warning: â‚œrankâ‚„ may be used
>>>>>>>>>>>> uninitialized in this function mpicc ‚  ‚ -O3
>>>>>>>>>>>> -Wall -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  accel.o accel.c mpicc ‚  ‚ -O3 -Wall -DPERIODIC
>>>>>>>>>>>> ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  read_ic.o read_ic.c read_ic.c: In function
>>>>>>>>>>>> â‚œfind_filesâ‚„:
>>>>>>>>>>>> read_ic.c:649:
>>>>>>>>>>>> warning: ignoring return value of
>>>>>>>>>>>> â‚œfreadâ‚„, declared
>>>>>>>>>>>> with attribute warn_unused_result read_ic.c:650:
>>>>>>>>>>>> warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:651: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:652: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:655: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:656: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:657: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:681: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:682: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:683: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:684: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:687: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:688: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c:689: warning:
>>>>>>>>>>>> ignoring return value of â‚œfreadâ‚„,
>>>>>>>>>>>> declared with attribute warn_unused_result
>>>>>>>>>>>> read_ic.c: In function
>>>>>>>>>>>> â‚œread_fileâ‚„:
>>>>>>>>>>>> read_ic.c:260: warning: â‚œhdf5_fileâ‚„ may
>>>>>>>>>>>> be used uninitialized in this function
>>>>>>>>>>>> read_ic.c:261: warning:
>>>>>>>>>>>> â‚œhdf5_datatypeâ‚„ may be used
>>>>>>>>>>>> uninitialized in this function mpicc ‚  ‚ -O3
>>>>>>>>>>>> -Wall -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  ngb.o ngb.c mpicc ‚  ‚ -O3 -Wall -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  system.o system.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  allocate.o allocate.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC
>>>>>>>>>>>> ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  density.o density.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  gravtree.o gravtree.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC
>>>>>>>>>>>> ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  hydra.o hydra.c mpicc ‚  ‚ -O3 -Wall -DPERIODIC
>>>>>>>>>>>> ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  driftfac.o driftfac.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC
>>>>>>>>>>>> ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  domain.o domain.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  allvars.o allvars.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  potential.o potential.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  forcetree.o forcetree.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  peano.o peano.c mpicc ‚  ‚ -O3 -Wall -DPERIODIC
>>>>>>>>>>>> ‚
>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  gravtree_forcetest.o gravtree_forcetest.c mpicc ‚
>>>>>>>>>>>>  ‚
>>>>>>>>>>>> -O3
>>>>>>>>>>>> -Wall
>>>>>>>>>>>> -DPERIODIC
>>>>>>>>>>>> ‚ -DUNEQUALSOFTENINGS -DPEANOHILBERT
>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128 -DSYNCHRONIZATION
>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.6.9/hdf5/include ‚
>>>>>>>>>>>>  -c -o
>>>>>>>>>>>>  pm_periodic.o pm_periodic.c pm_periodic.c:21:28:
>>>>>>>>>>>> error:
>>>>>>>>>>>> srfftw_mpi.h: No such file
>>>>>>>>>>>> or directory pm_periodic.c:34: error: expected
>>>>>>>>>>>> ₜ=₄,
>>>>>>>>>>>> ₜ,₄, ₜ;₄,
>>>>>>>>>>>> ₜasm₄ or ₜ__attribute__₄
>>>>>>>>>>>> before â‚œfft_forward_planâ‚„
>>>>>>>>>>>> pm_periodic.c:45: error:
>>>>>>>>>>>> expected ₜ=₄, ₜ,₄,
>>>>>>>>>>>> ₜ;₄, ₜasm₄ or
>>>>>>>>>>>> ₜ__attribute__₄ before ₜ*₄
>>>>>>>>>>>> token pm_periodic.c:46:
>>>>>>>>>>>> error: expected
>>>>>>>>>>>> ₜ=₄, ₜ,₄,
>>>>>>>>>>>> ₜ;₄, ₜasm₄ or
>>>>>>>>>>>> ₜ__attribute__₄ before ₜ*₄
>>>>>>>>>>>> token pm_periodic.c: In
>>>>>>>>>>>> function â‚œpm_init_periodicâ‚„:
>>>>>>>>>>>> pm_periodic.c:65:
>>>>>>>>>>>> error:
>>>>>>>>>>>> â‚œfft_forward_planâ‚„ undeclared (first
>>>>>>>>>>>> use in this function) pm_periodic.c:65: error: (Each
>>>>>>>>>>>> undeclared identifier is reported only once
>>>>>>>>>>>> pm_periodic.c:65:
>>>>>>>>>>>> error: for
>>>>>>>>>>>> each function it appears in.) pm_periodic.c:65:
>>>>>>>>>>>> warning:
>>>>>>>>>>>>  implicit declaration of function
>>>>>>>>>>>> â‚œrfftw3d_mpi_create_planâ‚„
>>>>>>>>>>>> pm_periodic.c:66: error:
>>>>>>>>>>>> â‚œFFTW_REAL_TO_COMPLEXâ‚„ undeclared
>>>>>>>>>>>> (first use in
>>>>>>>>>>>> this function) pm_periodic.c:66: error:
>>>>>>>>>>>> â‚œFFTW_ESTIMATEâ‚„ undeclared (first use
>>>>>>>>>>>> in this function) pm_periodic.c:66: error:
>>>>>>>>>>>> â‚œFFTW_IN_PLACEâ
>>>>>>>>>>>> ‚„ undeclared (first use in this function)
>>>>>>>>>>>> pm_periodic.c:67:
>>>>>>>>>>>> error:
>>>>>>>>>>>> â‚œfft_inverse_planâ‚„ undeclared (first
>>>>>>>>>>>> use in this function) pm_periodic.c:68: error:
>>>>>>>>>>>> â‚œFFTW_COMPLEX_TO_REALâ‚„ undeclared
>>>>>>>>>>>> (first use in
>>>>>>>>>>>> this function) pm_periodic.c:72: warning: implicit
>>>>>>>>>>>> declaration of function
>>>>>>>>>>>> â‚œrfftwnd_mpi_local_sizesâ‚„
>>>>>>>>>>>> pm_periodic.c: In function
>>>>>>>>>>>> â‚œpm_init_periodic_allocateâ‚„:
>>>>>>>>>>>> pm_periodic.c:124: error: â‚œrhogridâ‚„
>>>>>>>>>>>> undeclared (first
>>>>>>>>>>>> use in this function) pm_periodic.c:124: error:
>>>>>>>>>>>> â‚œfftw_realâ‚„ undeclared (first use in
>>>>>>>>>>>> this function)  pm_periodic.c:124:
>>>>>>>>>>>> error: expected
>>>>>>>>>>>> expression before ₜ)₄ token
>>>>>>>>>>>> pm_periodic.c:132:
>>>>>>>>>>>> error:
>>>>>>>>>>>> â‚œforcegridâ‚„ undeclared (first use in
>>>>>>>>>>>> this function) pm_periodic.c:132: error:
>>>>>>>>>>>> expected expression before ₜ)₄ token
>>>>>>>>>>>> pm_periodic.c:139:
>>>>>>>>>>>> error:
>>>>>>>>>>>> â‚œworkspaceâ‚„ undeclared (first use in
>>>>>>>>>>>> this function) pm_periodic.c:139: error: expected
>>>>>>>>>>>> expression before ₜ)₄ token
>>>>>>>>>>>> pm_periodic.c:153: error:
>>>>>>>>>>>> â‚œfft_of_rhogridâ‚„ undeclared (first use
>>>>>>>>>>>> in this function) pm_periodic.c:153: error:
>>>>>>>>>>>> â‚œfftw_complexâ‚„
>>>>>>>>>>>> undeclared (first use in this function)
>>>>>>>>>>>> pm_periodic.c:153:
>>>>>>>>>>>> error:
>>>>>>>>>>>> expected expression before ₜ)₄ token
>>>>>>>>>>>> pm_periodic.c:
>>>>>>>>>>>> In
>>>>>>>>>>>> function â‚œpm_init_periodic_freeâ‚„:
>>>>>>>>>>>> pm_periodic.c:163:
>>>>>>>>>>>>  error: â‚œworkspaceâ‚„ undeclared (first
>>>>>>>>>>>> use in this function) pm_periodic.c:164: error:
>>>>>>>>>>>> â‚œforcegridâ‚„ undeclared (first use in
>>>>>>>>>>>> this function)  pm_periodic.c:165:
>>>>>>>>>>>> error: â‚œrhogridâ‚„
>>>>>>>>>>>> undeclared (first use in this function)
>>>>>>>>>>>> pm_periodic.c:
>>>>>>>>>>>> In
>>>>>>>>>>>> function â‚œpmforce_periodicâ‚„:
>>>>>>>>>>>> pm_periodic.c:246:
>>>>>>>>>>>> error:
>>>>>>>>>>>> â‚œworkspaceâ‚„ undeclared (first use in
>>>>>>>>>>>> this function) pm_periodic.c:284: error:
>>>>>>>>>>>> â‚œrhogridâ‚„
>>>>>>>>>>>> undeclared (first use in this function)
>>>>>>>>>>>> pm_periodic.c:330:
>>>>>>>>>>>> error: â‚œfftw_realâ‚„
>>>>>>>>>>>> undeclared (first use in this function)
>>>>>>>>>>>> pm_periodic.c:331:
>>>>>>>>>>>> error:
>>>>>>>>>>>> â‚œforcegridâ‚„ undeclared (first use in
>>>>>>>>>>>> this function) pm_periodic.c:375: warning: implicit
>>>>>>>>>>>> declaration of function â‚œrfftwnd_mpiâ‚„
>>>>>>>>>>>> pm_periodic.c:375: error:
>>>>>>>>>>>> â‚œfft_forward_planâ‚„ undeclared (first
>>>>>>>>>>>> use in this function) pm_periodic.c:375: error:
>>>>>>>>>>>> â‚œFFTW_TRANSPOSED_ORDERâ‚„ undeclared
>>>>>>>>>>>> (first use in
>>>>>>>>>>>> this function) pm_periodic.c:426: error:
>>>>>>>>>>>> â‚œfft_of_rhogridâ‚„ undeclared (first use
>>>>>>>>>>>> in this function) pm_periodic.c:436: error:
>>>>>>>>>>>> â‚œfft_inverse_planâ‚„ undeclared (first
>>>>>>>>>>>> use in this function) pm_periodic.c: In function
>>>>>>>>>>>> â‚œpmpotential_periodicâ‚„:
>>>>>>>>>>>> pm_periodic.c:755: error: â‚œworkspaceâ‚„
>>>>>>>>>>>> undeclared (first
>>>>>>>>>>>> use in this function) pm_periodic.c:793: error:
>>>>>>>>>>>> â‚œrhogridâ‚„ undeclared (first use in
>>>>>>>>>>>> this function) pm_periodic.c:839:
>>>>>>>>>>>> error: â‚œfftw_realâ‚„
>>>>>>>>>>>> undeclared (first use in this function)
>>>>>>>>>>>> pm_periodic.c:840:
>>>>>>>>>>>> error:
>>>>>>>>>>>> â‚œforcegridâ‚„ undeclared (first use in
>>>>>>>>>>>> this function) pm_periodic.c:886: error:
>>>>>>>>>>>> â‚œfft_forward_planâ‚„
>>>>>>>>>>>> undeclared (first use in this function)
>>>>>>>>>>>> pm_periodic.c:886:
>>>>>>>>>>>> error:
>>>>>>>>>>>> â‚œFFTW_TRANSPOSED_ORDERâ‚„ undeclared
>>>>>>>>>>>> (first use in
>>>>>>>>>>>> this function) pm_periodic.c:934: error:
>>>>>>>>>>>> â‚œfft_of_rhogridâ‚„ undeclared (first use
>>>>>>>>>>>> in this function) pm_periodic.c:944: error:
>>>>>>>>>>>> â‚œfft_inverse_planâ‚„ undeclared
>>>>>>>>>>>> (first
>>>>>>>>>>>> use in this function) make: *** [pm_periodic.o]
>>>>>>>>>>>> Error 1
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Dimitry
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, September 9, 2009 18:00, Jay Billings
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> Ah, this error is much more subtle than the
>>>>>>>>>>>>> others. :)
>>>>>>>>>>>>> I
>>>>>>>>>>>>> believe this one is caused by using the wrong
>>>>>>>>>>>>> version of the HDF5 library. You are probably ‚
>>>>>>>>>>>>> using version 1.8.2 and need something like
>>>>>>>>>>>>>  version 1.6.2.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> There were some updates to the HDF5 API when they
>>>>>>>>>>>>> did  version 1.8.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Jay
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Wed, Sep 9, 2009 at 5:20 PM, Dimitry Ayzenberg
>>>>>>>>>>>>> <dayzenbe_at_andrew.cmu.edu>wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> So I think I have all the libraries and
>>>>>>>>>>>>>> whatever else I need properly installed and
>>>>>>>>>>>>>> linked. But when I run make I get an odd error
>>>>>>>>>>>>>> that I have ‚ no idea how to fix. This is the
>>>>>>>>>>>>>> full display when I do "make":
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> dimitry_at_Phoenix:~/Desktop/Gadget-2.0.4/Gadget2$
>>>>>>>>>>>>>> sudo make mpicc ‚  ‚ -O3 -Wall -DPERIODIC
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128
>>>>>>>>>>>>>> -DSYNCHRONIZATION
>>>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.8.3/hdf5/include
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -c
>>>>>>>>>>>>>> -o
>>>>>>>>>>>>>> main.o main.c mpicc ‚  ‚ -O3 -Wall -DPERIODIC
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128
>>>>>>>>>>>>>> -DSYNCHRONIZATION
>>>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.8.3/hdf5/include
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -c
>>>>>>>>>>>>>> -o
>>>>>>>>>>>>>> run.o run.c run.c: In function
>>>>>>>>>>>>>> â‚œrunâ‚„: run.c:102:
>>>>>>>>>>>>>>  warning:
>>>>>>>>>>>>>> ignoring return value of â‚œsystemâ‚„,
>>>>>>>>>>>>>> declared with  attribute warn_unused_result
>>>>>>>>>>>>>> mpicc ‚  ‚ -O3 -Wall -DPERIODIC
>>>>>>>>>>>>>> -DUNEQUALSOFTENINGS -DPEANOHILBERT
>>>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128
>>>>>>>>>>>>>> -DSYNCHRONIZATION
>>>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.8.3/hdf5/include
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -c
>>>>>>>>>>>>>> -o
>>>>>>>>>>>>>> predict.o predict.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>>>> -DPERIODIC
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128
>>>>>>>>>>>>>> -DSYNCHRONIZATION
>>>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.8.3/hdf5/include
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -c
>>>>>>>>>>>>>> -o
>>>>>>>>>>>>>> begrun.o begrun.c begrun.c: In function
>>>>>>>>>>>>>> â‚œread_parameter_fileâ‚„:
>>>>>>>>>>>>>> begrun.c:602: warning: ignoring return value of
>>>>>>>>>>>>>> â‚œfgetsâ‚„, declared with attribute
>>>>>>>>>>>>>> warn_unused_result begrun.c:653: warning:
>>>>>>>>>>>>>> ignoring return value of â‚œsystemâ‚„,
>>>>>>>>>>>>>> declared with  attribute warn_unused_result
>>>>>>>>>>>>>> mpicc ‚  ‚ -O3 -Wall -DPERIODIC
>>>>>>>>>>>>>> ‚ -DUNEQUALSOFTENINGS -DPEANOHILBERT
>>>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128
>>>>>>>>>>>>>> -DSYNCHRONIZATION
>>>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.8.3/hdf5/include
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -c
>>>>>>>>>>>>>> -o
>>>>>>>>>>>>>> endrun.o endrun.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128
>>>>>>>>>>>>>> -DSYNCHRONIZATION
>>>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.8.3/hdf5/include
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -c
>>>>>>>>>>>>>> -o
>>>>>>>>>>>>>> global.o global.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>>>> -DPERIODIC ‚
>>>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128
>>>>>>>>>>>>>> -DSYNCHRONIZATION
>>>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.8.3/hdf5/include
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -c
>>>>>>>>>>>>>> -o
>>>>>>>>>>>>>> timestep.o timestep.c mpicc ‚  ‚ -O3 -Wall
>>>>>>>>>>>>>> -DPERIODIC
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128
>>>>>>>>>>>>>> -DSYNCHRONIZATION
>>>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.8.3/hdf5/include
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -c
>>>>>>>>>>>>>> -o
>>>>>>>>>>>>>> init.o init.c mpicc ‚  ‚ -O3 -Wall -DPERIODIC
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -DUNEQUALSOFTENINGS
>>>>>>>>>>>>>> -DPEANOHILBERT
>>>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128
>>>>>>>>>>>>>> -DSYNCHRONIZATION
>>>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.8.3/hdf5/include
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -c
>>>>>>>>>>>>>> -o
>>>>>>>>>>>>>> restart.o restart.c restart.c: In function
>>>>>>>>>>>>>> â‚œrestartâ‚„:
>>>>>>>>>>>>>> restart.c:78:
>>>>>>>>>>>>>> warning: ignoring return value of
>>>>>>>>>>>>>> â‚œsystemâ‚„,
>>>>>>>>>>>>>> declared with attribute warn_unused_result mpicc
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -O3 -Wall
>>>>>>>>>>>>>> -DPERIODIC
>>>>>>>>>>>>>> -DUNEQUALSOFTENINGS -DPEANOHILBERT
>>>>>>>>>>>>>> -DWALLCLOCK ‚  ‚ -DPMGRID=128
>>>>>>>>>>>>>> -DSYNCHRONIZATION
>>>>>>>>>>>>>> -DHAVE_HDF5
>>>>>>>>>>>>>> -I/usr/local/include -I/usr/local/include
>>>>>>>>>>>>>> -I/home/dimitry/Desktop/hdf5-1.8.3/hdf5/include
>>>>>>>>>>>>>> ‚
>>>>>>>>>>>>>> -c
>>>>>>>>>>>>>> -o
>>>>>>>>>>>>>> io.o io.c io.c: In function
>>>>>>>>>>>>>> â‚œwrite_fileâ‚„:
>>>>>>>>>>>>>> io.c:774:
>>>>>>>>>>>>>> error: too
>>>>>>>>>>>>>> few arguments to function
>>>>>>>>>>>>>> â‚œH5Gcreate2â‚„ io.c:781:
>>>>>>>>>>>>>>  error:
>>>>>>>>>>>>>> too few arguments to function
>>>>>>>>>>>>>> â‚œH5Gcreate2â‚„
>>>>>>>>>>>>>> io.c:880:
>>>>>>>>>>>>>> error: too few arguments to function
>>>>>>>>>>>>>> â‚œH5Dcreate2â‚„ io.c: In function
>>>>>>>>>>>>>> â‚œwrite_header_attributes_in_hdf5â‚„:
>>>>>>>>>>>>>> io.c:1005: error: too few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„ io.c:1012: error: too
>>>>>>>>>>>>>> few arguments  to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„ io.c:1019: error: too
>>>>>>>>>>>>>> few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„
>>>>>>>>>>>>>> io.c:1027:
>>>>>>>>>>>>>> error:
>>>>>>>>>>>>>> too few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„
>>>>>>>>>>>>>> io.c:1033:
>>>>>>>>>>>>>> error: too
>>>>>>>>>>>>>> few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„
>>>>>>>>>>>>>> io.c:1039:
>>>>>>>>>>>>>> error:
>>>>>>>>>>>>>> too few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„
>>>>>>>>>>>>>> io.c:1045:
>>>>>>>>>>>>>> error: too few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„ io.c:1051: error: too
>>>>>>>>>>>>>> few arguments  to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„ io.c:1057: error: too
>>>>>>>>>>>>>> few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„
>>>>>>>>>>>>>> io.c:1063:
>>>>>>>>>>>>>> error:
>>>>>>>>>>>>>> too few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„
>>>>>>>>>>>>>> io.c:1069:
>>>>>>>>>>>>>> error: too
>>>>>>>>>>>>>> few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„
>>>>>>>>>>>>>> io.c:1075:
>>>>>>>>>>>>>> error:
>>>>>>>>>>>>>> too few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„
>>>>>>>>>>>>>> io.c:1081:
>>>>>>>>>>>>>> error: too few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„ io.c:1087: error: too
>>>>>>>>>>>>>> few arguments  to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„ io.c:1093: error: too
>>>>>>>>>>>>>> few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„
>>>>>>>>>>>>>> io.c:1099:
>>>>>>>>>>>>>> error:
>>>>>>>>>>>>>> too few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„
>>>>>>>>>>>>>> io.c:1108:
>>>>>>>>>>>>>> error: too
>>>>>>>>>>>>>> few arguments to function
>>>>>>>>>>>>>> â‚œH5Acreate2â‚„ make: ***
>>>>>>>>>>>>>>  [io.o]
>>>>>>>>>>>>>> Error 1
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Can someone please help me?
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>> Dimitry
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> -----------------------------------------------
>>>>>>>>>>>>>> ----
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> ----
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> If you wish to unsubscribe from this mailing,
>>>>>>>>>>>>>> send mail to minimalist_at_MPA-Garching.MPG.de with
>>>>>>>>>>>>>> a subject of: ‚ unsubscribe gadget-list A
>>>>>>>>>>>>>> web-archive of this mailing list is available
>>>>>>>>>>>>>> here:
>>>>>>>>>>>>>> http://www.mpa-garching.mpg.de/gadget/gadget-lis
>>>>>>>>>>>>>> t
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Dimitry Ayzenberg
>>>>>>>>>>>> Carnegie Mellon University
>>>>>>>>>>>> Physics - Class of 2012
>>>>>>>>>>>> Cell:(732)-425-4534
>>>>>>>>>>>> Email: dayzenbe_at_andrew.cmu.edu
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ---------------------------------------------------
>>>>>>>>>>>> ----
>>>>>>>>>>>> --
>>>>>>>>>>>> --
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> If you wish to unsubscribe from this mailing, send
>>>>>>>>>>>> mail  to minimalist_at_MPA-Garching.MPG.de with a
>>>>>>>>>>>> subject of: ‚  unsubscribe gadget-list A
>>>>>>>>>>>> web-archive of this mailing list is available here:
>>>>>>>>>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Dimitry Ayzenberg
>>>>>>>>>> Carnegie Mellon University
>>>>>>>>>> Physics - Class of 2012
>>>>>>>>>> Cell:(732)-425-4534
>>>>>>>>>> Email: dayzenbe_at_andrew.cmu.edu
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> -------------------------------------------------------
>>>>>>>>>> ----
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> If you wish to unsubscribe from this mailing, send mail
>>>>>>>>>> to minimalist_at_MPA-Garching.MPG.de with a subject of:
>>>>>>>>>> unsubscribe gadget-list A web-archive of this mailing
>>>>>>>>>> list is available here:
>>>>>>>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Dimitry Ayzenberg
>>>>>>>>> Carnegie Mellon University
>>>>>>>>> Physics - Class of 2012
>>>>>>>>> Cell:(732)-425-4534
>>>>>>>>> Email: dayzenbe_at_andrew.cmu.edu
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ---------------------------------------------------------
>>>>>>>>> --
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> If you wish to unsubscribe from this mailing, send mail
>>>>>>>>> to minimalist_at_MPA-Garching.MPG.de with a subject of:
>>>>>>>>>  unsubscribe
>>>>>>>>>  gadget-list A web-archive of this mailing list is
>>>>>>>>> available here:
>>>>>>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Dimitry Ayzenberg
>>>>>>>> Carnegie Mellon University
>>>>>>>> Physics - Class of 2012
>>>>>>>> Cell:(732)-425-4534
>>>>>>>> Email: dayzenbe_at_andrew.cmu.edu
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -----------------------------------------------------------
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> If you wish to unsubscribe from this mailing, send mail to
>>>>>>>> minimalist_at_MPA-Garching.MPG.de with a subject of:
>>>>>>>>  unsubscribe
>>>>>>>> gadget-list A web-archive of this mailing list is available
>>>>>>>> here:
>>>>>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Dimitry Ayzenberg
>>>>>>> Carnegie Mellon University
>>>>>>> Physics - Class of 2012
>>>>>>> Cell:(732)-425-4534
>>>>>>> Email: dayzenbe_at_andrew.cmu.edu
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> If you wish to unsubscribe from this mailing, send mail to
>>>>>>> minimalist_at_MPA-Garching.MPG.de with a subject of:
>>>>>>>  unsubscribe
>>>>>>> gadget-list A web-archive of this mailing list is available
>>>>>>> here:
>>>>>>>  http://www.mpa-garching.mpg.de/gadget/gadget-list
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Dimitry Ayzenberg
>>>>> Carnegie Mellon University
>>>>> Physics - Class of 2012
>>>>> Cell:(732)-425-4534
>>>>> Email: dayzenbe_at_andrew.cmu.edu
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -----------------------------------------------------------
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> If you wish to unsubscribe from this mailing, send mail to
>>>>> minimalist_at_MPA-Garching.MPG.de with a subject of:  unsubscribe
>>>>> gadget-list A web-archive of this mailing list is available here:
>>>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Dimitry Ayzenberg
>>> Carnegie Mellon University
>>> Physics - Class of 2012
>>> Cell:(732)-425-4534
>>> Email: dayzenbe_at_andrew.cmu.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>> -----------------------------------------------------------
>>>
>>>
>>>
>>> If you wish to unsubscribe from this mailing, send mail to
>>> minimalist_at_MPA-Garching.MPG.de with a subject of:  unsubscribe
>>> gadget-list  A web-archive of this mailing list is available here:
>>> http://www.mpa-garching.mpg.de/gadget/gadget-list
>>>
>>>
>>>
>>>
>>
>>
>> --
>> Dimitry Ayzenberg
>> Carnegie Mellon University
>> Physics - Class of 2012
>> Cell:(732)-425-4534
>> Email: dayzenbe_at_andrew.cmu.edu
>>
>>
>>
>>
>>
>> -----------------------------------------------------------
>>
>>
>> If you wish to unsubscribe from this mailing, send mail to
>> minimalist_at_MPA-Garching.MPG.de with a subject of:  unsubscribe
>> gadget-list A web-archive of this mailing list is available here:
>> http://www.mpa-garching.mpg.de/gadget/gadget-list
>>
>>
>
>


-- 
Dimitry Ayzenberg
Carnegie Mellon University
Physics - Class of 2012
Cell:(732)-425-4534
Email: dayzenbe_at_andrew.cmu.edu
Received on 2009-09-11 05:14:39

This archive was generated by hypermail 2.3.0 : 2022-09-01 14:03:42 CEST