ADIOS Users Manual 1.2.1
User Manual:
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Page Count: 94
ORNL/TM-2009/100
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ADIOS 1.2.1 User’s Manual
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August 2010
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This report was prepared as an account of work sponsored by an agency of the United States
Government. Neither the United States government nor any agency thereof, nor any of their employees,
makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy,
completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents
that its use would not infringe privately owned rights. Reference herein to any specific commercial
product, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily
constitute or imply its endorsement, recommendation, or favoring by the United States Government or any
agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect
those of the United States Government or any agency thereof.
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ORNL/TM-2009/100
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Prepared for the
Office of Science
U.S. Department of Energy
S. Hodson, S. Klasky, Q. Liu, J. Lofstead, N. Podhorszki, F. Zheng, M. Wolf,
T. Kordenbrock, H. Abbasi, N. Samatova
Aug. 2010
Prepared by
OAK RIDGE NATIONAL LABORATORY
Oak Ridge, Tennessee 37831-6070
managed by
UT-BATTELLE, LLC
for the
U.S. DEPARTMENT OF ENERGY
under contract DE-AC05-00OR22725
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http://www.nccs.gov/user-support/adios
626 F.,'G!$)/*4554*,()!
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,5(,c!&=L!7=(,&''!,+5!./-01!'7D9&9Ic!+5&L59!A7'5(c!&=L!(:;;%9,!;9%?9&S(#!!
cd trunk/
./configure –prefix=<install-dir> --with-mxml=<mxml-location>
make
make install
T%,5b! 4+595! 7(! &! runconf! D&,8+! (897;,! 7=! ,+5! ,9:=F! (5,! :;! A%9! %:9! S&8+7=5(#!
1,:LI7=?! 7,! 8&=! +5';! I%:! (5,,7=?! :;! ,+5! &;;9%;97&,5! 5=Z79%=S5=,! Z&97&D'5(! &=L!
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62620 H,).I!'5./*<+!
4+5! A%''%[7=?! 7(! &! (=&;(+%,! %A! ,+5! D&,8+! (897;,(! %=! ^[%Fc! &=! -=,5'MD&(5L!
-=A7=7D&=L!8':(,59!9:==7=?!G7=:Hb!
export MPICC=mpicc
export MPIFC=mpif90
export CC=pgcc
export FC=pgf90
export CFLAGS=”-fPIC”
./configure --prefix = <location for ADIOS software installation>
--with-mxml=<location of mini-xml installation>
--with-hdf5=<location of HDF5 installation>
--with-netcdf=<location of netCDF installation>
!
4+5!8%S;7'59!;%7=,5L!DI!KQ-<<!7(!:(5L!,%!D:7'L!&''!,+5!;&9&''5'!8%L5(!&=L!,%%'(!
:(7=?!KQ-c![+7'5!,+5!8%S;7'59!;%7=,5L!DI!<<!7(!:(5L!,%!D:7'L!,+5!(5O:5=,7&'!,%%'(#!
-=!;9&8,785c!S;788!:(5(!,+5!8%S;7'59!;%7=,5L!DI!<<!&=L!&LL(!,+5!KQ-!'7D9&9I!
&:,%S&,78&''I#!0=!8':(,59(c!,+7(!S&F5(!=%!95&'!L7AA595=85c!D:,!%=!6':5?5=5c!%9!<9&I!
J4c!;&9&''5'!8%L5(!&95!D:7',!A%9!8%S;:,5!=%L5(c![+7'5!,+5!(5O:5=,7&'!,%%'(!&95!D:7',!
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62626 ?+4J!K;D!
4%!7=(,&''!./-01!%=!&!<9&I!J4Bc!,+5!97?+,!8%S;7'59!8%SS&=L(!&=L!8%=A7?:95!A'&?(!
=55L!,%! D5! (5,#! 4+5! 95O:795L! 8%SS&=L(!A%9! ./-01! 7=(,&''&,7%=! %=!h&?:&9! &95! &(!
A%''%[(b!
>!
export CC=cc
export FC=ftn
./configure --prefix = <location for ADIOS software installation>
--with-mxml=<location of mini-xml installation>
--with-hdf5=<location of HDF5 installation>
--with-netcdf=<location of netCDF installation>
6262: &.>>(+*!C(+!L4*54-!
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95'%8&,&D'5!8%L5(c!(%!I%:!=55L!,%!&LL!,+5!nAQ-<!A'&?!,%!<@G.$1!D5A%95!8%=A7?:97=?!
./-01#!4+5!S&,'&D!95&L59!7(!=%,!D:7',!&:,%S&,78&''I!&,!S&F5!&=L!7(!=%,!7=(,&''5L!
[7,+!./-01#!j%:! =55L!,%!8%S;7'5! 7,![7,+!K&,'&Dk(! K^J!8%S;7'59! &A,59! ,+5!S&F5!
&=L!8%;I!,+5!A7'5(!S&=:&''I!,%!(%S5[+595![+595!K&,'&D!8&=!(55!,+5S#!
cd tools/matlab
make matlab
!
62: "#$%&!#<><)1<)',</!
62:20 L,),MKLH!>4+/<+!N+<O.,+<1P!
4+5!K7=7MJKG!'7D9&9I!7(!:(5L!,%!;&9(5!JKG!8%=A7?:9&,7%=!A7'5(#!K7=7MJKG!8&=!D5!
L%[='%&L5L!A9%S!!
http://www.minixml.org/software.php
62:26 LQ$!4)1!LQ$M$%!N+<O.,+<1P!
KQ-!&=L!KQ-M-0!7(!95O:795L!A%9!,+5!./-01!"#)!95'5&(5#!
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[+78+! =55L(! ,%! D5! 95,975Z5L! DI! ,+5! 859,&7=! KQ-! .Q-(c! 7(! 8%SS%='I! :(5L! 7=!
L5A7=7=?! ,+5! %:,;:,! A7'5(#! KQ-M-0! 8&=! &'(%! D5! 8%=(7L595L! ,+5! S%(,! ?5=5978! -]0!
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62:2: B(+*+4)RE!'(S>,5<+!N(>*,()45P!
4+5!@%9,9&=!RC!7=,59A&85!&=L!5H&S;'5!8%L5(!&95!8%S;7'5L!%='I!7A!,+595!7(!&=!ARC!
8%S;7'59!&Z&7'&D'5#!6I!L5A&:',!7,!7(!95O:795L!D:,!I%:!8&=!L7(&D'5!7,![7,+!,+5!%;,7%=!
--disable-fortran#!
62:2@ &<+,45!T<*?#BM:!N(>*,()45P!
4+5!bp2ncd!8%=Z59,59!:,7'7,I!,%!T5,</@!A%9S&,!7(!D:7',!%='I!7A!T5,</@!7(!&Z&7'&D'5#!!
<:995=,'I! ./-01! :(5(! ,+5! T5,</@M3! '7D9&9I#! _(5! ,+5! %;,7%=!
--with-netcdf=<path>!%9!5=(:95!,+&,! ,+5!T^4</@`/-Y!5=Z79%=S5=,!Z&97&D'5!
7(!(5,!D5A%95!8%=A7?:97=?!./-01#!
B!
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4+5! bp2h5! 8%=Z59,59! :,7'7,I! ,%! U/@B! A%9S&,! 7(! D:7',! %='I! 7A! &! U/@B! '7D9&9I! 7(!
&Z&7'&D'5#!<:995=,'I!./-01!:(5(!,+5!"#V!Z59(7%=!%A!,+5!U/@B!.Q-!D:,!7,!8&=!D5!D:7',!
&=L! :(5L! [7,+! ,+5! "#X#H! Z59(7%=! %A! ,+5! U/@B! '7D9&9I! ,%%#! _(5! ,+5! %;,7%=!
--with-hdf5=<path>![+5=!8%!
=A7?:97=?!./-01#!
62:2V QU#BD!N(>*,()45P!
4+5!,9&=(;%9,!S5,+%L![97,7=?!A7'5(!7=!,+5!Q&9&''5'! U/@B! A%9S&,!7(!D:7',!%='I!7A!&!
;&9&''5'!Z59(7%=!%A!,+5!U/@B!'7D9&9I!7(!N&'(%P!&Z&7'&D'5#!j%:!=55L!,%!:(5!,+5!%;,7%=!
--with-phdf5=<path>!,%!D:7'L!,+7(!,9&=(;%9,!S5,+%L#!!
-A! I%:! L5A7=5! Q&9&''5'! U/@B! &=L! L%! =%,! L5A7=5! (597&'! U/@Bc! ,+5=! D;)+B! [7''! D5!
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CC C compiler command
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CPP C preprocessor
CXX C++ compiler command
CXXFLAGS C++ compiler flags
FC Fortran compiler command
FCFLAGS Fortran compiler flags
CXXCPP C++ preprocessor
F77 Fortran 77 compiler command
FFLAGS Fortran 77 compiler flags
MPICC MPI C compiler command
MPIFC MPI Fortran compiler command
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/*example of parallel MPI write into a single file */
#include <stdio.h> // ADIOS header file required
#include ”adios.h”
int main (int argc, char *argv[])
{
int i, rank, NX;
double t [NX];
// ADIOS variables declaration
int64_t handle;
uint_64 total_size;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Init ( &argc, &argv);
MPI_Comm_rank (comm, &rank);
// data initialization
for ( i=0; i<NX; i++)
t [i] = i * (rank+1) + 0.1;
// ADIOS routines
adios_init ( “config.xml”);
adios_open (&handle, “temperature”, “data.bp”, “w”,&comm);
adios_group_size (handle, 4, total_size);
adios_write (handle, ”NX”, &NX);
adios_write (handle, ”temperature”, t);
adios_close (handle);
adios_finalize (rank);
MPI_Finalize();
return 0;
}
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adios_open(...);
adios_group_size(...);
……
//do your computation
……
adios_write(..);
adios_write(..);
adios_close(..);
!
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char path[1024];
adios_init ("config.xml");
adios_open (&adios_handle, "atoms", filename, "w", &comm);
sprintf(path, “node_%d_”, myrank);
adios_set_path(adios_handle, path);
#include "gwrite_atoms.ch"
adios_close (adios_handle);
adios_finalize (myrank);
!
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!
while [ ! –f conf ]; do
echo “Waiting for servers to start-up”
sleep 2s
done
while read line; do
export set “${line}”
done < conf
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V2620 41,(/Z<++S/A!]!41,(/Z<++)(!
int adios_errno
char * adios_errmsg()
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V2626 41,(/ZC(><)!!
ADIOS_FILE * adios_fopen (const char * fname, MPI_Comm comm)
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V262: 41,(/ZC'5(/<!
int adios_fclose (ADIOS_FILE *fp)
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V262@ 41,(/ZA(><)!]!41,(/ZA(><)Z-J,1!
ADIOS_GROUP * adios_gopen (ADIOS_FILE *fp, const char * grpname)
ADIOS_GROUP * adios_gopen_byid (ADIOS_FILE *fp, int grpid)
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V262D 41,(/ZA'5(/<!
int adios_gclose (ADIOS_GROUP *gp)
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V262V 41,(/Z,)OZ^4+!]!41,(/Z,)OZ^4+Z-J,1!
ADIOS_VARINFO * adios_inq_var (ADIOS_GROUP *gp, const char * varname)
ADIOS_VARINFO * adios_inq_var_byid (ADIOS_GROUP *gp, int varid)
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V262W 41,(/ZC+<<Z^4+,)C(!
void adios_free_varinfo (ADIOS_VARINFO *cp)
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V262X 41,(/Z+<41Z^4+!]!41,(/Z+<41Z^4+Z-J,1!
int64_t adios_read_var (ADIOS_GROUP * gp,
const char * varname,
const uint64_t * start,
const uint64_t * count,
void * data)
int64_t adios_read_var_byid (ADIOS_GROUP * gp,
int varid,
const uint64_t * start,
const uint64_t * count,
void * data)
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V262R 41,(/ZA<*Z4**+!]!41,(/ZA<*Z4**+Z-J,1!
int adios_get_attr (ADIOS_GROUP * gp,
const char * attrname,
enum ADIOS_DATATYPES * type,
int * size,
void ** data)
int adios_get_attr_byid (ADIOS_GROUP * gp,
int attrid,
enum ADIOS_DATATYPES * type,
int * size,
void ** data)
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V2620E 41,(/Z*J><Z*(Z/*+,)A!
const char * adios_type_to_string (enum ADIOS_DATATYPES type)
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V26200 41,(/Z*J><Z/,[<!
int adios_type_size(enum ADIOS_DATATYPES type, void *data)
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ADIOS_VARINFO * viy,
char * characteristic,
uint32_t time_start,
uint32_t time_end,
uint32_t lag)
double adios_stat_cov (ADIOS_VARINFO * vix,
ADIOS_VARINFO * viy,
char * characteristic,
uint32_t time_start,
uint32_t time_end,
uint32_t lag)
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&=L!3!,7S5(!:=L59!,+5!=&S5!]Z&9]7=,`HI,#!!
$ bpls -latv g_2x2_2x2_t3.bp
File info:
of groups: 1
of variables: 11
of attributes: 7
time steps: 3 starting from 1
file size: 779 KB
bp version: 1
endianness: Little Endian
Group genarray:
integer /dimensions/X scalar = 4
integer /dimensions/Y scalar = 4
integer /info/nproc scalar = 4
string /info/nproc/description attr = "Number of writers"
integer /info/npx scalar = 2
string /info/npx/description attr = "Number of processors
in x dimension"
integer /info/npy scalar = 2
string /info/npy/description attr = "Number of processors
in y dimension"
integer /var/int_xy {4, 4} = 0 / 15
string /var/int_xy/description attr = "2D array with 2D
decomposition"
integer /var/int_xyt {3, 4, 4} = 0 / 15
string /var/int_xyt/description attr = "3D array with 2D
decomposition with time in 3rd dimension"
!
B,A.+<!6E2!->5/!.*,5,*J!
4+5!8%=,5=,!%A!]Z&9]7=,`HI!8&=!D5!L:S;5L
B3!
(0,0) 0 1 2 3
(1,0) 4 5 6 7
(2,0) 8 9 10 11
(3,0) 12 13 14 15
4+5!l85=,9&'m!)H)!(:D(5,!%A!]Z&9]7=,`HI!8&=!D5!L:S;5L![7,+!
$ bpls g_2x2_2x2_t3.bp -d -s "1,1" -c "2,2" -n 2 var/int_xy
integer /var/int_xy {4, 4}
slice (1:2, 1:2)
(1,1) 5 6
(2,1) 9 10
4+5!'&(,!5'5S5=,!%A!]Z&9]7=,`HI,!A%9!5&8+!,7S5(,5;!8&=!D5!L:S;5L![7,+!
$ bpls g_2x2_2x2_t3.bp -d -s "0,-1,-1" -c "-1,1,1" -n 1 var/int_xyt
integer /var/int_xyt {3, 4, 4}
slice (0:2, 3:3, 3:3)
(0,3,3) 15
(1,3,3) 15
(2,3,3) 15
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python gpp.py <config_fname>
0E20 3\+,*<]A+<41]+<41!
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adios_write (adios_handle, “temperature”, t);
[+7'5!?95&L`[5&,+59#8+!8%=,&7=(!
adios_read (adios_handle, “temperature”, t_read).
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L7S5=(7%=(vmTJm!read=”no”]t!
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adios_write (adios_handle, “temperature”, temperature)
adios_read (adios_handle, “temperature”, t_read).
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adios_write (adios_handle, “temperature”, t)
adios_read (adios_handle, “temperature”, temperature)
0E26 "11!'()1,*,()45!<I>+<//,()!
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if (mype==0) {
adios_write (adios_handle, “temperature”, t)
}
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$ mpirun -np 4 1_nonadios_example
$ ls restart_*
restart_00000.dat restart_00001.dat restart_00002.dat
restart_00003.dat
!
0026 ?()/*+.'*!4)!KLH!B,5<!!
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!
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$ mpirun -np 4 2_adios_write
$ ls restart.bp
restart.bp
restart.bp.dir:
restart.bp.0 restart.bp.1 restart.bp.2 restart.bp.3
$ bpls -lad restart.bp.dir/restart.bp.2 -n 10
integer /NX scalar = 10
double /temperature {10} = 20 / 29
(0) 20 21 22 23 24 25 26 27 28 29
string /temperature/description attr = "Temperature array"
!
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$ ls restart.bp
restart.bp
$ bpls -l restart.bp
Group temperature:
integer /NX scalar = 10
double /temperature {10} = 0 / 39
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7=!&''!;9%85((5(!&=L!&''![7,+!,+5!(&S5!Z&':5#!4+5!%AA(5,!%A!&!'%8&'!&99&I![97,,5=!DI!
&!;9%85((!7(!L5A7=5L!:(7=?!,+5!9&=F!Z&97&D'5c![+78+!7(!L7AA595=,!%=!5Z59I!;9%85((#!
4+5!Z&97&D'5!7,(5'A!7(!L5A7=5L!&(!&=!"HTJ!,[%!L7S5=(7%=&'!&99&Ic!&',+%:?+!7=!,+5!<!
8%L5!7,!7(!(,7''!&!%=5!L7S5=(7%=&'!&99&I#!!
!
4+5!?[97,5!+5&L59!A7'5!?5=59&,5L!DI!?;;#;I!7(!,+5!A%''%[7=?b!
!
]q!?[97,5`,5S;59&,:95#8+!q]!
&L7%(`?9%:;(7a5!v!>!„!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!d!>!„!
VW!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!d!>!„!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!d!X!q!N"P!q!NTJPg!
&L7%(`?9%:;`(7a5!N&L7%(`+&=L'5c!&L7%(`?9%:;(7a5c!~&L7%(`,%,&'(7a5Pg!
&L7%(`[97,5!N&L7%(`+&=L'5c!pTJpc!~TJPg!
&L7%(`[97,5!N&L7%(`+&=L'5c!p(7a5pc!~(7a5Pg!
&L7%(`[97,5!N&L7%(`+&=L'5c!p9&=Fpc!~9&=FPg!
&L7%(`[97,5!N&L7%(`+&=L'5c!p,5S;59&,:95pc!,Pg!
!
B,A.+<!:E2!A\+,*<!8<41<+!C,5<!A<)<+4*<1!C+(S!'()C,A2IS5!
4+5!;9%?9&S!8%L5!7(!=%,!Z59I!L7AA595=,!A9%S!,+5!%=5!:(5L!7=!,+5!&D%Z5!5H&S;'5#!-,!
=55L(! ,%! +&Z5! ,+5! (7a5! &=L! 9&=F! Z&97&D'5(! 7=! ,+5! 8%L5! L5A7=5L! N(55!
5H&S;'5(]<]?'%D&'M&99&I]&L7%(`?'%D&'#8P!!
002X20 LQ$M$%!*+4)/>(+*!S<*8(1!NQ!\+,*<+/d!0!C,5<P!
$ mpirun -np 4 ./adios_global
$ ls adios_global.bp
adios_global.bp
$ bpls -latd adios_global.bp -n 10
integer /NX scalar = 10
integer /rank scalar = 0
integer /size scalar = 4
double /temperature {4, 10} = 0 / 39 / 19.5 /
11.5434 {MIN / MAX / AVG / STD_DEV}
(0,0) 0 1 2 3 4 5 6 7 8 9
(1,0) 10 11 12 13 14 15 16 17 18 19
(2,0) 20 21 22 23 24 25 26 27 28 29
(3,0) 30 31 32 33 34 35 36 37 38 39
!!(,97=?! ! ! ! ! ],5S;59&,:95]L5(897;,7%=! ! &,,9! ! ! v! p$'%D&'! &99&I! [97,,5=! A9%S! z(7a5z!
;9%85((5(p!
4+5!D;)=8L!:,7'7,I!8&=!D5!:(5L!,%!8%=Z59,!,+5!D;!A7'5!,%!&=!T5,</@!A7'5b!
!
$ bp2ncd adios_global.bp
$ ncdump adios_global.nc
netcdf adios_global {
dimensions:
NX = 10 ;
size = 4 ;
rank = 1 ;
variables:
double temperature(size, NX) ;
temperature:description = "Global array written
from \'size\' processes" ;
data:
VX!
temperature =
0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27, 28, 29,
30, 31, 32, 33, 34, 35, 36, 37, 38, 39 ;
}
002X26 Q%&$K!*+4)/>(+*!S<*8(1!NQ!\+,*<+/d!Q!&.-C,5</!e!0!L<*414*4!C,5<P!
4%! '7(,! Z&97&D'5(! %:,;:,! A9%S! Q01-J! ,9&=(;%9,c! :(59! %='I! =55L(! ,%! (;587AI! ,+5!
?'%D&'! S5,&L&,&! A7'5! N5#?#c! &L7%(`?'%D&'#D;P! &(! &! ;&9&S5,59! ,%! D;'(c! =%,! 5&8+!
7=L7Z7L:&'! A7'5(! N5#?#c! &L7%(`?'%D&'#D;#L79]&L7%(`?'%D&'#D;#CP#! 4+5! %:,;:,! %A! ,+5!
Q01-J!&=L!,+5!KQ-!S5,+%L(!&95!5O:7Z&'5=,!A9%S!95&L7=?!;%7=,!%A!Z75[#!!
$ mpirun -np 4 ./adios_global
$ ls adios_global.bp
adios_global.bp
$ bpls -latd adios_global.bp -n 10
integer /NX scalar = 10
integer /rank scalar = 0
integer /size scalar = 4
double /temperature {4, 10} = 0 / 39 / 19.5 /
11.5434 {MIN / MAX / AVG / STD_DEV}
(0,0) 0 1 2 3 4 5 6 7 8 9
(1,0) 10 11 12 13 14 15 16 17 18 19
(2,0) 20 21 22 23 24 25 26 27 28 29
(3,0) 30 31 32 33 34 35 36 37 38 39
!!(,97=?!!!!!],5S;59&,:95]L5(897;,7%=!!&,,9!!!v!p$'%D&'!&99&I![97,,5=!A9%S!z(7a5z!
;9%85((5(p!
4+5!5H&S;'5(]<]?'%D&'M&99&I]&L7%(`95&L`?'%D&'#8!;9%?9&S!(+%[(!+%[!,%!:(5!,+5!
?5=5978!95&L!.Q-!,%!95&L!7=!,+5!?'%D&'!&99&I!A9%S!&9D7,9&9I!=:SD59!%A!;9%85((5(#!!
002R 7+,*,)A!;,S<M$)1<I!,)*(!4!`4+,4-5<!
4+5!,7S5M7=L5H!&''%[(!,+5!:(59!,%!L5A7=5!&!Z&97&D'5![7,+!&=!:='7S7,5L!L7S5=(7%=c!
&'%=?![+78+!,+5!Z&97&D'5!8&=!?9%[!7=!,7S5#!G5,k(!(:;;%(5!,+5!:(59![&=,(!,%![97,5!
%:,! ,5S;59&,:95! &A,59! &! 859,&7=! =:SD59! %A! 7,59&,7%=(#! @79(,c! [5! &LL! ,+5! l,7S5M
7=L5Hm! &,,97D:,5! ,%! ,+5! &L7%(M?9%:;! [7,+! &=! &9D7,9&9I! =&S5c! 5#?#! l7,59m#! T5H,c! [5!
A7=L! ,+5! N?'%D&'P! Z&97&D'5! ,5S;59&,:95! 7=! ,+5! &L7%(M?9%:;! &=L! &LL! l7,59m! &(! &=!
5H,9&!L7S5=(7%=!A%9!7,g!,+5!958%9L!=:SD59!A%9!,+&,!Z&97&D'5![7''!D5!(,%95L!5Z59I!
,7S5!7,!?5,(![97,,5=!%:,#!T%,5!,+&,![5!L%!=%,!=55L!,%!8+&=?5!,+5!L7S5=(7%=(!&=L!
%AA(5,(!7=!,+5!?'%D&'!D%:=L(c!%='I!,+5!7=L7Z7L:&'!Z&97&D'5#!.'(%!=%,5c!,+&,!,+5!,7S5!
L7S5=(7%=!S:(,!D5!,+5!('%[5(,!8+&=?7=?!L7S5=(7%=c!7#5#!7=!<c!,+5!A79(,!%=5!&=L!7=!
@%9,9&=c!7,!S:(,!D5!,+5!'&(,!%=5#!
!
]q!8%=A7?#HS'q]!
s&L7%(M8%=A7?!+%(,M'&=?:&?5vp<pt!
VR!
!!!!s&L7%(M?9%:;!=&S5vp,5S;59&,:95p!8%%9L7=&,7%=M8%SS:=78&,%9vp8%SSp!,7S5M
7=L5Hvm;457mt!
!!!!!!!!sZ&9!=&S5vpTJp!,I;5vp7=,5?59p]t!
!!!!!!!!sZ&9!=&S5vp(7a5p!,I;5vp7=,5?59p]t!
!!!!!!!!sZ&9!=&S5vpF5Ip!,I;5vp7=,5?59p]t!
!!!!!!!!s?'%D&'MD%:=L(!L7S5=(7%=(vp(7a5cTJp!%AA(5,(vpF5IcCpt!
!!!!!!!!!!!!sZ&9!=&S5vp,5S;59&,:95p!?[97,5vp,p!,I;5vpL%:D'5p!!
!!!!!!!!!!!!!!!!!!!!!!L7S5=(7%=(vp;457c"cTJp]t!!!!h/245i&D27&F2747<3i&l;457`&35586&42&V5&
J94&;3&4K5&538i&;(5(i&8;G536;23_`/Ci'i;457`j!
!!!!!!!!s]?'%D&'MD%:=L(t!
!!!!!!!!s&,,97D:,5!=&S5vpL5(897;,7%=p!;&,+vp],5S;59&,:95p!!
!!!!!!!!!!!!Z&':5vp$'%D&'!&99&I![97,,5=!A9%S!z(7a5z!;9%85((5(!%Z59!(5Z59&'!,7S5(,5;(p!!
!!!!!!!!!!!!,I;5vp(,97=?p]t!
!!!!s]&L7%(M?9%:;t!
sS5,+%L!?9%:;vp,5S;59&,:95p!S5,+%LvpKQ-p]t!
sD:AA59!(7a5MK6vp"p!&''%8&,5M,7S5vp=%[p]t!
s]&L7%(M8%=A7?t!
!
B,A.+<!:02!?()C,A2IS5!C(+!4!A5(-45!4++4J!\,*8!*,S<!
N<I4S>5</]?]A5(-45M4++4JM*,S<]41,(/ZA5(-45*,S<2IS5P!
4+5! 5H&S;'5(]<]?'%D&'M&99&IM,7S5]&L7%(`?'%D&',7S5#8! 7(! (7S7'&9! ,%! ,+5! ;95Z7%:(!
5H&S;'5! &L7%(`?'%D&'#8! 8%L5#! 4+5! %='I! L7AA595=85! 7(! ,+&,! 7,! +&(! &=! 7,59&,7%=! '%%;!
[+595!5&8+!;9%85((
WC!
(5,3,0) 630 631 632 633 634 635 636 637 638 639
(6,0,0) 700 701 702 703 704 705 706 707 708 709
(6,1,0) 710 711 712 713 714 715 716 717 718 719
(6,2,0) 720 721 722 723 724 725 726 727 728 729
(6,3,0) 730 731 732 733 734 735 736 737 738 739
0020E Y<41,)A!/*4*,/*,'/!
-=!.L7%(!"#)c!(,&,7(,78(!'7F5!S7=7S:Sc!S&H7S:Sc!&Z59&?5!&=L!(,&=L&9L!L5Z7&,7%=!
8&=!D5!&??95?&,5L!7=5H;5=(7Z5'I#!4+7(!(58,7%=!(+%[(!+%[!,+5(5!(,&,7(,78(!8&=!D5!
&885((5L! A9%S! ,+5! 6Q! A7'5#! 4+5! 5H&S;'5(]<](,&,](,&,`[97,5#8! 7(! (7S7'&9! ,%! ,+5!
;95Z7%:(!5H&S;'5!&L7%(`?'%D&',7S5#8#!-,![97,5(!&=!&LL7,7%=&'!Z&97&D'5!l8%S;'5Hm!%A!
,I;5! &L7%(`L%:D'5`8%S;'5H! &'%=?! [7,+! l,5S;59&,:95#m! ! -,! &'(%! +&(! +7(,%?9&S!
5=&D'5L! A%9! ,+5! Z&97&D'5! l,5S;59&,:95#m! ! <%S;&97=?! 7,! [7,+! ,+5! JKG! 7=! ,+5!
;95Z7%:(!5H&S;'5c!(,&,#HS'!+&(!,+5!A%''%[7=?!&LL7,7%=(b!
!
]q!(,&,#HS'q]!
!
s2HS'!Z59(7%=vp"#Cp2t!
s&L7%(M8%=A7?!+%(,M'&=?:&?5vp<pt!
!! s&L7%(M?9%:;!=&S5vp,5S;59&,:95p!8%%9L7=&,7%=M8%SS:=78&,%9vp8%SSp!!
,7S5M7=L5Hvp7,59pt!
!! ! sZ&9!=&S5vpTJp!,I;5vp7=,5?59p]t!
!! ! sZ&9!=&S5vp9&=Fp!,I;5vp7=,5?59p]t!
!! ! sZ&9!=&S5vp(7a5p!,I;5vp7=,5?59p]t!
!! ! s?'%D&'MD%:=L(!L7S5=(7%=(vp(7a5cTJp!%AA(5,(vp9&=FcCpt!
!! ! ! sZ&9!=&S5vp,5S;59&,:95p!?[97,5vp,p!,I;5vpL%:D'5p!
!! ! ! ! L7S5=(7%=(vp7,59c"cTJp]t!
!! sP<7!=&S5vp8%S;'5Hp!?[97,5vp8p!4XJ5_k829V=5&:2GJ=5Uk&
!! ! ! ! L7S5=(7%=(vp7,59c"cTJp]t!
!! ! s]?'%D&'MD%:=L(t!
s]&L7%(M?9%:;t!
!
!! sS5,+%L!?9%:;vp,5S;59&,:95p!S5,+%LvpKQ-p]t!
!! sD:AA59!(7a5MK6vpBp!&''%8&,5M,7S5vp=%[p]t!
!! s<3<=X6;6!&L7%(M?9%:;vp,5S;59&,:95p!Z&9vp,5S;59&,:95p!
!! ! D95&FM;%7=,(vpCc!"CCc!"CCCc!"CCCCp!]t!
s]&L7%(M8%=A7?t!
!
B,A.+<!:62!?()C,A2IS5!C(+!'+<4*,)A!8,/*(A+4S!C(+!4)!4++4J!^4+,4-5<!
N<I4S>5</]?]/*4*]/*4*2IS5P!
!
4%!7=8':L5!+7(,%?9&S!8&'8:'&,7%=c!%='I!,+5!JKG!A7'5!=55L(!,%!D5!:;L&,5Lc!&=L!=%!
8+&=?5!7(!95O:795L!7=!,+5!<!8%L5#!4+5!5H&S;'5(]<](,&,]?[97,5`(,&,#8+!95O:795(!&=!
W"!
&LL7,7%=&'! X! q! N)P! q! TJ!,%!D5!&LL5L!,%!&L7%(`?9%:;(7a5!&=L!&=!&L7%(`[97,5!
N&L7%(`+&=L'5c!p8%S;'5Hpc!~8P!,%!+&=L'5!,+5!8%S;'5H!=:SD59(#!
$ mpirun -np 2 ./stat_write
[1]: adios_stat.bp written successfully
[0]: adios_stat.bp written successfully
4+5!5H&S;'5(]<](,&,](,&,`95&L#8!(+%[(!+%[!,%!95&L!D&8F!,+5!(,&,7(,78(!A9%S!,+5!
D;!A7'5#!@79(,c!,+5!(,&,7(,78(!=55L!,%!D5!;%;:'&,5L!7=,%!&=!./-01`\.Y-T@0!%De58,#!
4+7(!7(!L%=5![7,+!,+5!A%''%[7=?!(5,!%A!8%SS&=L(#!
ADIOS_FILE * f = adios_fopen ("adios_stat.bp", comm);
ADIOS_GROUP * g = adios_gopen (f, "temperature");
ADIOS_VARINFO * v = adios_inq_var (g, "temperature");
4+5! %De58,! •Zk! =%[! 8%=,&7=(! &''! ,+5! (,&,7(,78&'! 7=A%9S&,7%=! A%9! ,+5! Z&97&D'5!
l,5S;59&,:95#m! 4%! &885((! ,+5! +7(,%?9&S! A%9! ,5S;59&,:95c! [5! =55L! ,%! &885((! ,+5!
./-01`U-14! L&,&! (,9:8,:95! 7=(7L5! ,+5! ./-01`\.Y-T@0! %De58,#! 4+5! 8%L5! D5'%[!
;97=,(!,+5!D95&F!;%7=,(!&=L!,+5!7=,59Z&'!A95O:5=875(!A%9!,+5!?'%D&'!+7(,%?9&S#!@%9!
•=k!D95&F!;%7=,(!,+595!&95!•=!d!"k!7=,59Z&'(#!
/* Break points */
for (j = 0; j < v->hist->num_breaks; j++)
printf ("%lf ", v->hist->breaks[j]);
/* Frequencies */
for (j = 0; j <= v->hist->num_breaks; j++)
printf ("%d\t", v->hist->gfrequencies[j]);
adios_free_varinfo(v);
4%!&885((!,+5!(,&,7(,78(!95'&,5L!,%!,+5!Z&97&D'5!l8%S;'5Hcm![5!=55Lb!
v = adios_inq_var (g, "complex");
4+5!8%L5!D5'%[!L5(897D5(!+%[!,%!;97=,!,+5!S7=7S:S!Z&':5(!%A!,+5!S&?=7,:L5c!
95&'!&=L!7S&?7=&9I!;&9,!%A!8%S;'5H!L&,&!&,!5&8+!,7S5(,5;#!@%9!8%S;'5H!Z&97&D'5(!
&'%=5c!&''!(,&,7(,78(!=55L!,%!D5!,I;58&(,5L!7=,%!&!L%:D'5!A%9S&,#!
double ** Cmin = (double **) v->mins;
printf ("\nMagnitude Real Imaginary\n");
for (j = 0; v->ndim >= 0 && (j < v->dims[0]); j ++)
printf ("%lf %lf %lf\n",
Cmin[j][0], Cmin[j][1], Cmin[j][2]);
adios_free_varinfo(v);
!
W)!
06 #<^<5(><+!L4).45!
!
0620 ?+<4*<!T<\!;+4)/>(+*!L<*8(1/!
0=5!%A!./-01k(!7S;%9,&=,!A5&,:95(!7(!,+5!8%S;%=5=,7a&,7%=!%A!,9&=(;%9,!S5,+%L(#!
_(59(!8&=!([7,8+!&S%=?!,+5!,I;78&'!S5,+%L(!,+&,![5!(:;;%9,!%9!5Z5=!895&,5!,+579!
%[=! S5,+%L(c! [+78+! 8&=! D5! 5&(7'I! ;':??5L! 7=,%! %:9! '7D9&9I#! 4+5! A%''%[7=?!
(58,7%=(! ;9%Z7L5! ,+5! ;9%85L:95(! A%9! &LL7=?! ,+5! =5[! ,9&=(;%9,! S5,+%L! 8&''5L!
l&D8m! 7=,%! ,+5! ./-01! '7D9&9I#! -=! ,+7(! Z59(7%=! %A! ./-01c! &''! ,+5! (%:985! A7'5(! &95!
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062020 "11!*8<!)<\!S<*8(1!S4'+(/!,)!41,(/Z*+4)/>(+*Z8((G/28!!
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,9&=(;%9,! 7S;'5S5=,&,7%=! &=L! :(59! .Q-(#! -=! ,+5! A7'5c! [5! A79(,! A7=L! ,+5! '7=5! ,+&,!
L5A7=5(!,+5!5=:S59&,7%=!,I;5!.L7%(`-0`S5,+%L(`L&,&,I;5!&LL!,+5!L58'&9&,7%=!%A!
S5,+%L! -/! ./-01`K^4U0/`.6<c! &=Lc! D58&:(5! [5! &LL! &! =5[! S5,+%Lc! :;L&,5!
,%,&'!=:SD59!%A!,9&=(;%9,!S5,+%L(!./-01`K^4U0/`<0_T4!A9%S!R!,%!"C#!
"#!5=:S!.L7%(`-0`S5,+%L(!L&,&,I;5!!
5=:S!./-01`-0`K^4U0/!•!
!!!!!!!!!!!!!!!!!!!!!!./-01`K^4U0/`_TfT0*T!!!v!M)!
!!!!!!!!!!!!!!!!!!!!!c./-01`K^4U0/`T_GG!!!!!!!!!!!!!!v!M"!
!!!!!!!!!!!!!!!!!!!!!c./-01`K^4U0/`KQ-!!!!!!!!!!!!!!!!!v!C!
!!!!!!!!!!!!!!!!!!!!!uu!
!!!!!!!!!!!!!!!!!!!!!c./-01`K^4U0/`QU/@B!!!!!!!!!!!!v!X!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!./-01`K^4U0/`.6<!!v!R!
!!!!!!!!!!!!!!!!!!!!!c./-01`K^4U0/`<0_T4!!!!!!!!!!!v!R!!!!./-01`K^4U0/`<0_T4!!v!"C!
!!!!!!!!!!!!!!!!!!!!!‚g!
!
)#! T5H,c! [5! =55L! ,%! L58'&95! ,+5! ,9&=(;%9,! .Q-(! A%9! S5,+%L! l&D8cm! 7=8':L7=?!
7=7,]A7=&'7a5c! %;5=]8'%(5c! (+%:'L`D:AA59c! &=L! 95&L][97,5#! 17S7'&9! ,%! ,+5! %,+59!
S5,+%L(c![5!=55L!,%!&LL!!
!!!!!@0Y*.Y/`/^<G.Y^!N&D8P!
3#! 4+5=c! [5! &LL! ,+5! S&;;7=?! %A! ,+5! (,97=?! =&S5! l&D8m! %A! ,+5! =5[! ,9&=(;%9,!
S5,+%L!,%!,+5!S5,+%L!-/!M!./-01`K^4U0/`.6<c![+78+!+&(!D55=!&'95&LI!L5A7=5L!
7=!5=:S59&,7%=!,I;5!.L7%(`-0`S5,+%L(`L&,&,I;5#!.(!,+5!'&(,!;&9&S5,59c!l"m!+595!
S5&=(!,+5!S5,+%L!95O:795(!8%SS:=78&,7%=(c!%9!lCm!7A!=%,#!
!!!!!K.4<U`14Y-T$`40`K^4U0/!Np&D8pc!./-01`K^4U0/`.6<c!"P!!!!!!!!!!!!!!
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Function
Purpose
adios_init
Load the XML configuration file creating
internal representations of the various data
types and defining the methods used for
writing.
adios_finalize
Cleanup anything remaining before exiting
the code
adios_open
Prepare a data type for subsequent calls to
write data using the io_handle. Mode is one
of “r” (read), “w” (write) and “a” (append).
adios_close
Commit all the write to disk, close the file
and release adios file handle
adios_group_size
Passing the required buffer size to the
transport layer and returned the total size
back to the source code
adios_write
Submit a data element for writing. This does
NOT actually perform the write in buffered
mode. In the overflow case, this call writes to
buffer directly.
adios_read
Submit a buffer space (var) for reading a data
element into. This does NOT actually
perform the read. Actual population of the
buffer space will happen on the call to
adios_close
XB!
adios_set_path
Set the HDF5-style path for all variables in a
adios-group. This will reset whatever is
specified in the XML file.
adios_set_path_var
Set the HDF-5-style path for the specified
var in the group. This will reset whatever is
specified in the XML file.
adios_get_write_buffer
For the given field, get a buffer that will be
used at the transport level for it of the given
size. If size == 0, then auto calculate the
size based on what is known from the
datatype in the XML file and any provided
additional elements (such as array dimension
elements). To return this buffer, just do a
normal call to adios_write using the same
io_handle, field_name, and the returned
buffer.
adios_start_calculation
An indicator that it is now an ideal time to do
bulk data transfers as the code will not be
performing IO for a while.
adios_end_ calculation
An indicator that it is no longer a good time
to do bulk data transfers as the code is
about to start doing communication with
other nodes causing possible conflicts
adios_end_iteration
A tick counter for the IO routines to time
how fast they are emptying the buffers.
!
