outputting Gadget2 files in HDF5 format to visualize in yt
Hi, I am just starting to learn the SPH simulation code Gadget2, I followed this tutorial https://astrobites.org/2011/04/02/installing-and-running-gadget-2/ and succesfully ran the simulation and got some output files. However, I needed to comment out the -DHAVE HDF5 to avoid compilation error and now I have no good way to visualize my output. I srated with SPLASH but still trying to figure out how to deal with some error there. I figured out yt has analysis tool for Gadget outputs and I would very much love to try yt. I would very appreciate if anyone tells me how to get Gadget output in HDF5 formate. I am using ubuntu 16.04LTS. I need to know how to install HDF5 or necessary package in my machine to get the HDF5 output first. laso If you tell me a little how to change the Gadget Makefile for that, that would be very nice. I am quoting some excerpt from my Makefile. #--------------------------------------- Output OPT += -DHAVE_HDF5 #OPT += -DOUTPUTPOTENTIAL #OPT += -DOUTPUTACCELERATION #OPT += -DOUTPUTCHANGEOFENTROPY #OPT += -DOUTPUTTIMESTEP #---------------------------------------------------------------------- # Here, select compile environment for the target machine. This may need # adjustment, depending on your local system. Follow the examples to add # additional target platforms, and to get things properly compiled. #---------------------------------------------------------------------- #--------------------------------------- Select some defaults CC = mpicc # sets the C-compiler OPTIMIZE = -O2 -Wall -g # sets optimization and warning flags MPICHLIB = -lmpich #--------------------------------------- Select target computer SYSTYPE="trina" #SYSTYPE="Mako" #SYSTYPE="Regatta" #SYSTYPE="RZG_LinuxCluster" #SYSTYPE="RZG_LinuxCluster-gcc" #SYSTYPE="OpteronMPA" #SYSTYPE="OPA-Cluster32" #SYSTYPE="OPA-Cluster64" #--------------------------------------- Adjust settings for target computer ifeq ($(SYSTYPE),"trina") CC = mpicc OPTIMIZE = -O3 -Wall GSL_INCL = -I/usr/local/include GSL_LIBS = -L/usr/local/lib FFTW_INCL= -I/usr/local/include FFTW_LIBS= -L/usr/local/lib MPICHLIB = -L/usr/lib endif and sorry for spaming the yt list with Gadget2 stuff. thanks Turhan
Hi Turhan, There are numerous methods for installing the HDF5 libraries including conda ( http://conda.pydata.org/docs/install/quick.html#linux-miniconda-install) or just building hdf5 from source ( https://support.hdfgroup.org/HDF5/release/obtainsrc.html). Aside from that, I am not sure what to tell you about other help with installing gadget. After all, this is the yt mailing list, not the gadget help list. Looks like there is some info here: http://wwwmpa.mpa-garching.mpg.de/gadget/html/ . Good luck with the install! Cameron On Fri, Nov 18, 2016 at 4:01 PM, turhan nasri <turhannasri@gmail.com> wrote:
Hi, I am just starting to learn the SPH simulation code Gadget2, I followed this tutorial https://astrobites.org/2011/04/02/installing-and-running- gadget-2/ and succesfully ran the simulation and got some output files. However, I needed to comment out the -DHAVE HDF5 to avoid compilation error and now I have no good way to visualize my output. I srated with SPLASH but still trying to figure out how to deal with some error there.
I figured out yt has analysis tool for Gadget outputs and I would very much love to try yt. I would very appreciate if anyone tells me how to get Gadget output in HDF5 formate. I am using ubuntu 16.04LTS. I need to know how to install HDF5 or necessary package in my machine to get the HDF5 output first. laso If you tell me a little how to change the Gadget Makefile for that, that would be very nice. I am quoting some excerpt from my Makefile.
#--------------------------------------- Output OPT += -DHAVE_HDF5 #OPT += -DOUTPUTPOTENTIAL #OPT += -DOUTPUTACCELERATION #OPT += -DOUTPUTCHANGEOFENTROPY #OPT += -DOUTPUTTIMESTEP
#---------------------------------------------------------------------- # Here, select compile environment for the target machine. This may need # adjustment, depending on your local system. Follow the examples to add # additional target platforms, and to get things properly compiled. #----------------------------------------------------------------------
#--------------------------------------- Select some defaults
CC = mpicc # sets the C-compiler OPTIMIZE = -O2 -Wall -g # sets optimization and warning flags MPICHLIB = -lmpich
#--------------------------------------- Select target computer
SYSTYPE="trina" #SYSTYPE="Mako" #SYSTYPE="Regatta" #SYSTYPE="RZG_LinuxCluster" #SYSTYPE="RZG_LinuxCluster-gcc" #SYSTYPE="OpteronMPA" #SYSTYPE="OPA-Cluster32" #SYSTYPE="OPA-Cluster64"
#--------------------------------------- Adjust settings for target computer
ifeq ($(SYSTYPE),"trina") CC = mpicc OPTIMIZE = -O3 -Wall GSL_INCL = -I/usr/local/include GSL_LIBS = -L/usr/local/lib FFTW_INCL= -I/usr/local/include FFTW_LIBS= -L/usr/local/lib MPICHLIB = -L/usr/lib endif
and sorry for spaming the yt list with Gadget2 stuff. thanks Turhan
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-- Cameron Hummels NSF Postdoctoral Fellow Department of Astronomy California Institute of Technology http://chummels.org
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turhan nasri