Differences

This shows you the differences between two versions of the page.

--- howto:gadget-2 [2016/04/07 10:58]
sfebruary [Running Gadget2]
+++ howto:gadget-2 [2021/12/09 16:42] (current)
@@ Line 1: / Line 1: @@
 ====== Gadget2 at CHPC ======
+From its [[http://wwwmpa.mpa-garching.mpg.de/~volker/gadget/|website]]: "GADGET computes gravitational forces with a hierarchical tree algorithm (optionally in combination with a particle-mesh scheme for long-range gravitational forces) and represents fluids by means of smoothed particle hydrodynamics (SPH)... GADGET can therefore be used to address a wide array of astrophysically interesting problems, ranging from colliding and merging galaxies, to the formation of large-scale structure in the Universe. With the inclusion of additional physical processes such as radiative cooling and heating, GADGET can also be used to study the dynamics of the gaseous intergalactic medium, or to address star formation and its regulation by feedback processes."
 Contents:
   - [[gadget-2#compiling_your_own_gadget2_code|Compiling your own Gadget2 code]]
   - [[gadget-2#running_gadget2|Running Gadget2]]
+  - [[gadget-2#generating_initial_conditions|Generating Initial Conditions]]
 ===== Compiling your own Gadget2 code =====
@@ Line 31: / Line 33: @@
 export LD_LIBRARY_PATH=$UTILS_DIR/$FFTW_INSTALL/lib:$LD_LIBRARY_PATH
 </code>
+as well as add the appropriate "SYSTYPE", e.g.
+<code bash>
+#--------------------------------------- Select target computer
+SYSTYPE="CHPC"
+ifeq ($(SYSTYPE),"CHPC")
+CC       =  mpicc
+OPTIMIZE =  -O3 -Wall
+GSL_INCL =  -I/apps/chpc/astro/utils/gcc/v510-openmpi188/gsl-1.16-build/include
+GSL_LIBS =  -L/apps/chpc/astro/utils/gcc/v510-openmpi188/gsl-1.16-build/lib -lgsl -lgslcblas
+FFTW_INCL=  -I/apps/chpc/astro/utils/gcc/v510-openmpi188/fftw-2.1.5-build/include
+FFTW_LIBS=  -L/apps/chpc/astro/utils/gcc/v510-openmpi188/fftw-2.1.5-build/lib
+MPICHLIB =
+HDF5INCL =
+HDF5LIB  =
+endif
+</code>
 Finally, to compile:
 <code bash>
@@ Line 39: / Line 58: @@
 ===== Running Gadget2 =====
-Let's consider one of the examples provided in ''Gadget-2.0.7/Gadget2/parameterfiles/''.
+This assumes you have successfully compiled Gadget, have put together a parameter file for your particular simulation as well as generated the corresponding initial conditions. For now, let's consider one of the examples provided in ''Gadget-2.0.7/Gadget2/parameterfiles/'', say "LCDM gas".
+=== Step 1 ===
+Make sure that you create the necessary paths (and directories) for the storing of your input data (e.g. initial conditions) as well as for the saving of Gadget2 snapshots (and other information) somewhere **on the Lustre (scratch) filesystem** i.e. ''/mnt/lustre/users/username/''. Then, in ''Gadget-2.0.7/Gadget2/parameterfiles/lcdm_gas.param'' adjust the ''InitCondFile'' and ''OutputDir'' variables accordingly. If you intend to use a predetermined set of redshifts at which to write snapshots, also adjust ''OutputListFilename'' as required (usually a small file, but is regarded as input data).
+=== Step 2 ===
+Create a PBS script for the job and then submit the job to the cluster queue (see [[quick:start?#example_job_scripts|our quick start guide]] for such information) as follows:
+<code bash>
+[username@login1 ~]$ qsub mypbsjobscript.sh
+</code>
+===== Generating Initial Conditions =====
+If you require any help with generating your own initial conditions, please contact [[mailto:sfebruary@csir.co.za|Sean February]] or [[mailto:ccress@csir.co.za|Catherine Cress]].

wiki.chpc.ac.za

User Tools

Site Tools

Differences

Page Tools