Re: Error when doing make

From: Dimitry Ayzenberg <dayzenbe_at_andrew.cmu.edu>
Date: Wed, 9 Sep 2009 22:57:33 -0400

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
Received on 2009-09-10 04:57:36

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