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
Received on 2009-09-10 01:37:56