Re: Error when doing make

From: Scott Wales <wales_at_physics.usyd.edu.au>
Date: Thu, 10 Sep 2009 13:43:33 +1000

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 ‘run’: run.c:102: warning:
>>>>>>>> ignoring return value of ‘system’, 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
>>>>>>>> ‘read_parameter_file’:
>>>>>>>> begrun.c:602:
>>>>>>>> warning: ignoring return value of ‘fgets’, declared
>>>>>>>> with attribute warn_unused_result begrun.c:653: warning:
>>>>>>>> ignoring return value of ‘system’, 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 ‘restart’:
>>>>>>>> restart.c:78:
>>>>>>>> warning:
>>>>>>>> ignoring return value of ‘system’, 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 ‘write_file’:
>>>>>>>> io.c:687: warning: ‘rank’ 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 ‘find_files’:
>>>>>>>> read_ic.c:649:
>>>>>>>> warning: ignoring return value of ‘fread’, declared
>>>>>>>> with attribute warn_unused_result read_ic.c:650: warning:
>>>>>>>> ignoring return value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:651: warning: ignoring return
>>>>>>>> value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:652:
>>>>>>>> warning: ignoring return
>>>>>>>> value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:655: warning: ignoring return
>>>>>>>> value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:656: warning:
>>>>>>>> ignoring return value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:657: warning: ignoring return
>>>>>>>> value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:681:
>>>>>>>> warning: ignoring return
>>>>>>>> value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:682: warning: ignoring return
>>>>>>>> value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:683: warning:
>>>>>>>> ignoring return value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:684: warning: ignoring return
>>>>>>>> value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:687:
>>>>>>>> warning: ignoring return
>>>>>>>> value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:688: warning: ignoring return
>>>>>>>> value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c:689: warning:
>>>>>>>> ignoring return value of ‘fread’, declared with attribute
>>>>>>>> warn_unused_result read_ic.c: In function ‘read_file’:
>>>>>>>> read_ic.c:260: warning: ‘hdf5_file’ may be used
>>>>>>>> uninitialized in this function read_ic.c:261: warning:
>>>>>>>> ‘hdf5_datatype’ 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 ‘=’,
>>>>>>>> ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before
>>>>>>>> ‘fft_forward_plan’ pm_periodic.c:45: error: expected
>>>>>>>> ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
>>>>>>>> before ‘*’ token pm_periodic.c:46: error: expected
>>>>>>>> ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
>>>>>>>> before ‘*’ token pm_periodic.c:
>>>>>>>> In function ‘pm_init_periodic’:
>>>>>>>> pm_periodic.c:65: error: ‘fft_forward_plan’ 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 ‘rfftw3d_mpi_create_plan’
>>>>>>>> pm_periodic.c:66: error:
>>>>>>>> ‘FFTW_REAL_TO_COMPLEX’ undeclared (first use in this
>>>>>>>> function) pm_periodic.c:66: error: ‘FFTW_ESTIMATE’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:66:
>>>>>>>> error: ‘FFTW_IN_PLACE
>>>>>>>>
>>>>>>>> undeclared (first use in this function) pm_periodic.c:67:
>>>>>>>> error:
>>>>>>>> ‘fft_inverse_plan’ undeclared (first use in this function)
>>>>>>>> pm_periodic.c:68: error: ‘FFTW_COMPLEX_TO_REAL’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:72:
>>>>>>>> warning:
>>>>>>>> implicit declaration of function ‘rfftwnd_mpi_local_sizes’
>>>>>>>> pm_periodic.c: In function
>>>>>>>> ‘pm_init_periodic_allocate’:
>>>>>>>> pm_periodic.c:124: error: ‘rhogrid’ undeclared (first use
>>>>>>>> in this function) pm_periodic.c:124: error: ‘fftw_real’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:124:
>>>>>>>> error: expected
>>>>>>>> expression before ‘)’ token pm_periodic.c:132: error:
>>>>>>>> ‘forcegrid’ undeclared (first use in this function)
>>>>>>>> pm_periodic.c:132: error:
>>>>>>>> expected expression before ‘)’ token pm_periodic.c:139:
>>>>>>>> error:
>>>>>>>> ‘workspace’ undeclared (first use in this function)
>>>>>>>> pm_periodic.c:139: error: expected expression before ‘)’
>>>>>>>> token pm_periodic.c:153: error: ‘fft_of_rhogrid’
>>>>>>>> undeclared (first use
>>>>>>>> in this function) pm_periodic.c:153: error: ‘fftw_complex’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:153:
>>>>>>>> error:
>>>>>>>> expected expression before ‘)’ token pm_periodic.c: In
>>>>>>>> function ‘pm_init_periodic_free’: pm_periodic.c:163:
>>>>>>>> error: ‘workspace’ undeclared (first use
>>>>>>>> in this function) pm_periodic.c:164: error: ‘forcegrid’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:165:
>>>>>>>> error: ‘rhogrid’
>>>>>>>> undeclared (first use in this function) pm_periodic.c: In
>>>>>>>> function ‘pmforce_periodic’: pm_periodic.c:246: error:
>>>>>>>> ‘workspace’ undeclared (first use in this function)
>>>>>>>> pm_periodic.c:284: error: ‘rhogrid’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:330:
>>>>>>>> error: ‘fftw_real’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:331:
>>>>>>>> error:
>>>>>>>> ‘forcegrid’ undeclared (first use in this function)
>>>>>>>> pm_periodic.c:375: warning: implicit declaration of
>>>>>>>> function ‘rfftwnd_mpi’ pm_periodic.c:375: error:
>>>>>>>> ‘fft_forward_plan’ undeclared (first use in this
>>>>>>>> function) pm_periodic.c:375: error:
>>>>>>>> ‘FFTW_TRANSPOSED_ORDER’ undeclared (first use in this
>>>>>>>> function) pm_periodic.c:426: error: ‘fft_of_rhogrid’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:436:
>>>>>>>> error:
>>>>>>>> ‘fft_inverse_plan’ undeclared (first use in this function)
>>>>>>>> pm_periodic.c: In function
>>>>>>>> ‘pmpotential_periodic’:
>>>>>>>> pm_periodic.c:755: error: ‘workspace’ undeclared (first
>>>>>>>> use in this function) pm_periodic.c:793: error: ‘rhogrid’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:839:
>>>>>>>> error: ‘fftw_real’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:840:
>>>>>>>> error:
>>>>>>>> ‘forcegrid’ undeclared (first use in this function)
>>>>>>>> pm_periodic.c:886: error: ‘fft_forward_plan’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:886:
>>>>>>>> error:
>>>>>>>> ‘FFTW_TRANSPOSED_ORDER’ undeclared (first use in this
>>>>>>>> function) pm_periodic.c:934: error: ‘fft_of_rhogrid’
>>>>>>>> undeclared (first use in this function) pm_periodic.c:944:
>>>>>>>> error: ‘fft_inverse_plan’ 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 ‘run’: run.c:102:
>>>>>>>>>> warning:
>>>>>>>>>> ignoring return value of ‘system’, 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
>>>>>>>>>> ‘read_parameter_file’:
>>>>>>>>>> begrun.c:602: warning: ignoring return value of
>>>>>>>>>> ‘fgets’, declared with attribute warn_unused_result
>>>>>>>>>> begrun.c:653:
>>>>>>>>>> warning:
>>>>>>>>>> ignoring return value of ‘system’, 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 ‘restart’:
>>>>>>>>>> restart.c:78:
>>>>>>>>>> warning: ignoring return value of ‘system’, 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 ‘write_file’: io.c:774:
>>>>>>>>>> error: too
>>>>>>>>>> few arguments to function ‘H5Gcreate2’ io.c:781:
>>>>>>>>>> error:
>>>>>>>>>> too few arguments to function ‘H5Gcreate2’ io.c:880:
>>>>>>>>>> error: too few arguments to function ‘H5Dcreate2’
>>>>>>>>>> io.c: In function ‘write_header_attributes_in_hdf5’:
>>>>>>>>>> io.c:1005: error: too few arguments to function
>>>>>>>>>> ‘H5Acreate2’ io.c:1012: error: too few arguments to
>>>>>>>>>> function ‘H5Acreate2’ io.c:1019: error: too few
>>>>>>>>>> arguments to function ‘H5Acreate2’ io.c:1027: error:
>>>>>>>>>> too few arguments to function ‘H5Acreate2’ io.c:1033:
>>>>>>>>>> error: too
>>>>>>>>>> few arguments to function ‘H5Acreate2’ io.c:1039:
>>>>>>>>>> error:
>>>>>>>>>> too few arguments to function ‘H5Acreate2’ io.c:1045:
>>>>>>>>>> error: too few arguments to function
>>>>>>>>>> ‘H5Acreate2’ io.c:1051: error: too few arguments to
>>>>>>>>>> function ‘H5Acreate2’ io.c:1057: error: too few
>>>>>>>>>> arguments to function ‘H5Acreate2’ io.c:1063: error:
>>>>>>>>>> too few arguments to function ‘H5Acreate2’ io.c:1069:
>>>>>>>>>> error: too
>>>>>>>>>> few arguments to function ‘H5Acreate2’ io.c:1075:
>>>>>>>>>> error:
>>>>>>>>>> too few arguments to function ‘H5Acreate2’ io.c:1081:
>>>>>>>>>> error: too few arguments to function
>>>>>>>>>> ‘H5Acreate2’ io.c:1087: error: too few arguments to
>>>>>>>>>> function ‘H5Acreate2’ io.c:1093: error: too few
>>>>>>>>>> arguments to function ‘H5Acreate2’ io.c:1099: error:
>>>>>>>>>> too few arguments to function ‘H5Acreate2’ io.c:1108:
>>>>>>>>>> error: too
>>>>>>>>>> few arguments to function ‘H5Acreate2’ 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-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
Received on 2009-09-10 05:43:54

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