wiki:computo:flash []

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======INSTALACIÓN DE FLASH======

=====EN COMPUTADORA PERSONAL=====
1. Registrarse en la Universidad de Chicago: [[http://flash.uchicago.edu/|FLASH]]

2. Luego, se enviará por mail la aceptación y se podrá bajar el código: [[http://flash.uchicago.edu/|FLASH]]

3. Descomprimir el tar.gz bajado en el lugar donde se va a querer trabajar.

4. Instalar fortran, c, mpif90. Para éste último, instalar mpich.

5. Flash necesita la librería hdf5 1.8.12. Instalación como root: bajar, descomprimir, y hacer
<HTML>
<ul class="shell-body">
         <li style="color:greenyellow">&nbsp;&nbsp;./configure --prefix=/usr/local/hdf5</li>
         <li style="color:greenyellow"> </li>
         <li style="color:greenyellow"> </li>
         <li style="color:greenyellow">&nbsp;&nbsp;make</li>
         <li style="color:greenyellow"> </li>
         <li style="color:greenyellow"> </li>
         <li style="color:greenyellow">&nbsp;&nbsp;make install</li>
</ul>
<br>
</HTML>




=====EN LOS CLUSTERS=====
 1. Ya está instalado. Sólo levantar los módulos que se detallan en la sección “Uso de Flash”

----------------------------------

======USO DE FLASH======


Manual de usuario: [[http://flash.uchicago.edu/site/flashcode/user_support/|manual de FLASH]]


1. El Makefile.h que usa para compilar el programa está en:
 /lugardeinstalacion/FLASHX.X/sites/Prototypes/Linux
 Allí hay varios ejemplos de makefiles. Para nuestro ejemplo utilizaremos un makefile que llamaremos Makefile.h.escogido. Iremos a la carpeta "site".

<HTML>
<ul class="shell-body">
         <li style="color:greenyellow">&nbsp;&nbsp;cd /lugardeinstalacion/FLASHX.X/sites/</li>
</ul>
<br>
</HTML>
Ejecutar el siguiente comando.
<HTML>
<ul class="shell-body">
         <li style="color:greenyellow">&nbsp;&nbsp;mkdir $HOSTNAME</li>
</ul>
<br>
</HTML>
Eso creará una carpeta que se llama como el nombre de la maquina en /sites. Copiar en esa carpeta  el Makefile.h elegido. Renombrar este archivo a Makefile.h.
<HTML>
<ul class="shell-body">
         <li style="color:greenyellow">&nbsp;&nbsp;cd  /lugardeinstalacion/FLASHX.X/sites/Prototypes/Linux/ </li>
                  <li style="color:greenyellow">&nbsp;&nbsp;cp Makefile.h.elegido /lugardeinstalacion/FLASHX.X/sites/Makefile.h </li>
</ul>
<br>
</HTML>



2. Módulos a cargar en las diferentes máquinas:

<HTML>

<br>
<b>clemente</b>
<br>
<br>
<ul class="shell-body">
         <li style="color:greenyellow">&nbsp;&nbsp;module load gcc</li>
                  <li style="color:greenyellow">&nbsp;&nbsp;module load openmpi</li>
         <li style="color:greenyellow">&nbsp;&nbsp;module load hypre</li>
         <li style="color:greenyellow">&nbsp;&nbsp;module load hdf5</li>
         <li style="color:greenyellow">&nbsp;&nbsp;module load flash</li>
</ul>

<button class="botonPanel"  >Makefile.h</button>
<div class="panel">
         <br>
         <ul class="ul1">
            <li class="li1">Nombre del archivo: Makefile.h</li>
            <li class="li1">Servidor: clemente </li>
         </ul>    
         <br>
</HTML>       
<file c Makefile.h[enable_line_numbers="true",highlight_lines_extra="8,10,11,12"]>
#FLASH makefile definitions for x86-64 Linux (GNU compilers)
#----------------------------------------------------------------------------
# Set the HDF5/MPI library paths -- these need to be updated for your system
#----------------------------------------------------------------------------
#      sites/clemente/Makefile.h


MPI_PATH   = /opt/spack/0.16.2/opt/spack/linux-centos7-broadwell/gcc-10.2.0/openmpi-4.0.5-jdedu5ob5yuqtaujmqw7l3fyzfaatzqm/
HDF4_PATH  =
HDF5_PATH  = /opt/spack/0.16.2/opt/spack/linux-centos7-broadwell/gcc-10.2.0/hdf5-1.10.7-6v6h3jwmez6mhhfg5vrhp2odezq7kdat/
HYPRE_PATH = /opt/spack/0.16.2/opt/spack/linux-centos7-broadwell/gcc-10.2.0/hypre-2.20.0-izz4brayoocfvlz2u3z76avmrlvls2gi/
ZLIB_PATH  = /opt/spack/0.16.2/opt/spack/linux-centos7-broadwell/gcc-10.2.0/zlib-1.2.11-nk6k5unszfepso6b4zvivtimoeped7if/



PAPI_PATH  =
PAPI_FLAGS =

NCMPI_PATH = /usr/local/netcdf
MPE_PATH   =

#----------------------------------------------------------------------------
# Compiler and linker commands
#
#   Use the MPICH wrappers around the compilers -- these will automatically
#   load the proper libraries and include files.  Version of MPICH prior
#   to 1.2.2 (?) do not recognize .F90 as a valid Fortran file extension.
#   You need to edit mpif90 and add .F90 to the test of filename extensions,
#   or upgrade your MPICH.
#----------------------------------------------------------------------------

FCOMP   = ${MPI_PATH}/bin/mpif90
CCOMP   = ${MPI_PATH}/bin/mpicc
CPPCOMP = ${MPI_PATH}/bin/mpic++
LINK    = ${MPI_PATH}/bin/mpif90

# pre-processor flag
PP      = -D

#----------------------------------------------------------------------------
# Compilation flags
#
#  Three sets of compilation/linking flags are defined: one for optimized
#  code, one for testing, and one for debugging.  The default is to use the
#  _OPT version.  Specifying -debug to setup will pick the _DEBUG version,
#  these should enable bounds checking.  Specifying _TEST is used for
#  flash_test, and is set for quick code generation, and (sometimes)
#  profiling.  The Makefile generated by setup will assign the generic token
#  (ex. FFLAGS) to the proper set of flags (ex. FFLAGS_OPT).
#----------------------------------------------------------------------------

OPENMP =
#-fopenmp


#  *************************cambio ********************************
#        PATRON
#FFLAGS_OPT = -c -O2  -fdefault-real-8 -fdefault-double-8 \
#-Wuninitialized

#        OPTIMIZADO
FFLAGS_OPT = -c -O3 -march=broadwell -fdefault-real-8 -fdefault-double-8 \
-Wuninitialized

#I explictly add -O0 because I found that compiling source files without
#an optimization flag generates the same object code as compiling source
#files with -O2.  The -O0 is required so that gdb no longer shows
#"<value optimized out>" for certain function arguments.

FFLAGS_DEBUG = -ggdb -c -O0 -fdefault-real-8 -fdefault-double-8 \
-pedantic -Wall -Waliasing \
-Wsurprising -Wconversion -Wunderflow \
-ffpe-trap=invalid,zero,overflow -fbounds-check \
-fimplicit-none -fstack-protector-all

FFLAGS_TEST = -ggdb -c -O0 -fdefault-real-8 -fdefault-double-8

FFLAGS_HYPRE = -I${HYPRE_PATH}/include


F90FLAGS = -w -fallow-argument-mismatch


#The macro _FORTIFY_SOURCE adds some lightweight checks for buffer
#overflows at both compile time and run time (only active at -O1 or higher)
#http://gcc.gnu.org/ml/gcc-patches/2004-09/msg02055.html


#   *****************************cambios***********************************
#      FLAGS PATRON
#CFLAGS_OPT = -ggdb -c -O2 -Wuninitialized -D_FORTIFY_SOURCE=2

#      FLAGS OPTIMIZADO
CFLAGS_OPT = -c -O3 -march=broadwell -Wuninitialized -D_FORTIFY_SOURCE=2

CFLAGS_DEBUG = -ggdb -c -O0 -Wno-div-by-zero -Wundef \
-Wconversion -Wstrict-prototypes -Wunreachable-code \
-pedantic -Wall -Winit-self -ftree-vrp -Wfloat-equal \
-Wunsafe-loop-optimizations -Wpadded -fstack-protector-all

CFLAGS_TEST = -ggdb -O0 -c


# if we are using HDF5, we need to specify the path to the include files
CFLAGS_HDF5 = -I${HDF5_PATH}/include -DH5_USE_16_API
CFLAGS_NCMPI = -I${NCMPI_PATH}/include

#----------------------------------------------------------------------------
# Linker flags
#
#  There is a seperate version of the linker flags for each of the _OPT,
#  _DEBUG, and _TEST cases.
#----------------------------------------------------------------------------

LFLAGS_OPT   = -o
LFLAGS_DEBUG = -ggdb -O0 -o
LFLAGS_TEST  = -ggdb -O0 -o


#----------------------------------------------------------------------------
# Library specific linking
#
#  If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to
#  create a macro in this Makefile.h for LIB_xxx, which will be added to the
#  link line when FLASH is built.  This allows us to switch between different
#  (incompatible) libraries.  We also create a _OPT, _DEBUG, and _TEST
#  library macro to add any performance-minded libraries (like fast math),
#  depending on how FLASH was setup.
#----------------------------------------------------------------------------

LIB_OPT   =
LIB_DEBUG =
LIB_TEST  =

LIB_HDF4  =
LIB_HDF5  = -L ${HDF5_PATH}/lib -lhdf5 -lz

LIB_PAPI  =
LIB_MATH  =

LIB_MPI   =
LIB_NCMPI = -L ${NCMPI_PATH}/lib -lpnetcdf
LIB_MPE   =

LIB_HYPRE = -L${HYPRE_PATH}/lib -lHYPRE

# Uncomment the following line to use electic fence memory debugger.
# export EF_ALLOW_MALLOC_0=1
#CONFIG_LIB = -L/usr/lib64 -lefence

#----------------------------------------------------------------------------
# Additional machine-dependent object files
#
#  Add any machine specific files here -- they will be compiled and linked
#  when FLASH is built.
#----------------------------------------------------------------------------

MACHOBJ =

#----------------------------------------------------------------------------
# Additional commands
#----------------------------------------------------------------------------

MV = mv -f
AR = ar -r
RM = rm -f
CD = cd
RL = ranlib
ECHO = echo


#----------------------------------------------------------------------------
# Fake existence of iso_c_bindings module to prevent unnecessary recompilations.
#----------------------------------------------------------------------------
ifeq ($(FLASHBINARY),true)
iso_c_binding.mod :
    touch $@
endif
</file>
<HTML>  
</div>




<br>

<br>
<b>mulatona (mulatona.ccad.unc.edu.ar)</b>
<br>
<br>
<ul class="shell-body">
         <li style="color:greenyellow">&nbsp;&nbsp;module load gcc/7</li>
         <li style="color:greenyellow">&nbsp;&nbsp;module load flash/4.4</li>
</ul>
<br>
<b>mendieta (mendieta.ccad.unc.edu.ar)</b>
<br>
<br>
<ul class="shell-body">
         <li style="color:greenyellow">&nbsp;&nbsp;module load flash/4.5</li>
</ul>
<br>
</HTML>

3. Cómo compilar el programa:
 En /lugardeinstalacion/FLASHX.X/./setup magnetoHD/proyecto -auto -parfile=flash.par +usm threadBlockList=True -objdir=object -site=clemente -2d -maxblocks=5000 -nxb=20 -nyb=10


  * **parfile**: archivo de parámetros
  * **+usm**: se activa el Unsplit Staggered Method. Este metodo evalua los campos en las caras, para hacer una correcta limpieza de los monopolos magnéticos.
  * **threadBlockList**:
  * **-objdir**: directorio donde se crearán los objetos para compilar
  * **-site**: nombre de la máquina donde se correrá. Si no se pone nada, por default es la máquina donde estamos
  * **-2d**: corrida bidimensional
  * **maxblocks**: número máximo de bloques permitidos
  * **nxb, nyb**: número de celdas por bloque.


Luego compilar haciendo:

<HTML>
<ul class="shell-body">
         <li style="color:greenyellow">&nbsp;&nbsp;cd /lugardeinstalacion/FLASHX.X/object/ </li>
           <li style="color:greenyellow">&nbsp;&nbsp;make -j 16</li>
</ul>
<br>
<br>
</HTML>


4. Cómo correr el programa

a) Máquinas con trabajos en cola → clemente, mulatona (uso exclusivo del IATE) y mendieta (cluster UNC)
 Para correr el programa, usar los diferentes [[script>wiki:infraestructura_computo|script]] según la maquina . Se deben copiar los submit_job_maquina.sh en las carpetas donde se crean los objetos de la compilación. Luego correrlos con:
 sbatch submit_job_maquina.sh

<HTML>
  <i><tips class="tips">
Tips: antes de correr verificar los cores y nodos disponibles: </tips></i><br><br>
</HTML>
[[Tutorial>wiki:tutorial_slurm|Tutorial de Slurm]]


b) Para correr en las máquinas sin trabajos en cola:

<HTML>
<ul class="shell-body">
         <li style="color:greenyellow">&nbsp;&nbsp;cd /lugardeinstalacion/FLASHX.X/object/ </li>
           <li style="color:greenyellow">&nbsp;&nbsp;mpirun -np 8 ./flash4</li>

</ul>
<br>
</HTML>
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