Preparing tag 1.4

configure.ac: incr version number to 1.3.3 and bug-report address changed
Delete all files are benchmark is done.
2007-08-29 01:43:58 +00:00 · 2007-04-25 07:21:56 +00:00 · 2007-04-24 22:48:53 +00:00 · 2007-04-24 21:57:28 +00:00 · 2007-04-20 12:00:40 +00:00 · 2007-04-20 11:59:54 +00:00
12 changed files with 340 additions and 219 deletions
@@ -28,6 +28,7 @@ doc/H5PartVisIt/cloud_visit_2D.png -text
 doc/H5PartVisIt/cloud_visit_2D.s.png -text
 doc/H5PartVisIt/visit_query1.png -text
 doc/H5PartVisIt/visit_query1.s.png -text
+doc/H5X_File_Format.txt -text
 doc/H5tools/H5tools.html -text
 doc/H5tools/H5tools_files/snapshot1.jpg -text
 doc/InternalLayout.html -text
@@ -1,6 +1,6 @@
 # Every configure script must call AC_INIT before doing anything else.
 # AC_INIT (package, version, [bug-report], [tarname])
-AC_INIT([H5Part], [1.3.2], [vis@hpcrdm.lbl.gov], H5Part)
+AC_INIT([H5Part], [1.3.3], [h5part@lists.psi.ch], H5Part)


 # Ensure that a recent enough version of Autoconf is being used. 
@@ -6,8 +6,6 @@
 <meta name="keywords" content="scientific visualization">
 <meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">

-<!--#include virtual="/include/topIncludes.html"-->
-
 <div id="maincenter">


@@ -15,7 +13,7 @@
    <title>Building HDF5</title>
  </head>

-  <body bgcolor="#F0F0F0">
+  <body>
    <font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
    <UL>
      <LI><a href="#ConfigOptions">Configure Options</a>
@@ -64,5 +62,3 @@ source .tcshr (.cshrc, .bashrc) in the one that you are using.

 You can <a href="http://vis.lbl.gov/Research/AcceleratorSAPP/Downloading.html">continue <a/>downloading and installing H5Part.
 </div>
-
-<!--#include virtual="/include/dateFooter.html"-->
@@ -11,7 +11,7 @@
    <title>Downloading HDF5 and H5Part</title>

  </head>
-   <body bgcolor="#F0F0F0">
+   <body>
    <font face="arial,helvetica" size="+2" color="#555588"><h2>Downloading H5Part</h2></font>
    <UL>
      <LI><a href="#hdf5">Downloading HDF5</a>
@@ -21,63 +21,15 @@
    <hr>
    <a name="hdf5">
    <h2>Downloading HDF5</h2></a>
-	You will need to download and install the hdf5 library and link H5Part with it.
-	<pre>
-	ftp ftp.ncsa.uiuc.edu
-	username: anonymous
-	password: your email
-	cd HDF/HDF5/current/src
-	ls
-	get hdf5-1.6.5.tar.gz (get the current version, this as the one on April 20th, 2006)
-	cd szip/src
-	ls
-	get szip-2.0.tar.gz (get the current version, this as the one on April 20th, 2006)
-	cd ../../
-	cd zlib/1.2/src
-	ls
-	get zlib-1.2.1.tar.gz (get the current version, this as the one on April 20th, 2006)
-	</pre>
-
- <P>
-	Note: you might already have libz in your system and you will not need libsz unless you build hdf5 with support for it.
-</P>
-
-<h4>Building Parallel HDF5</h4>
-<P>
-When you build HDF5, you will need to build an version with parallel I/O
-enabled. Here is a set of configure options that worked for us on a
-Linux workstation running SuSE 10.1 with MPICH installed in /usr/local/mpich.
-</p>
-
-<pre>
-./configure --prefix=/usr/local/hdf5-mpich --enable-parallel CC=mpicc CXX=mpicxx --disable-shared --enable-static --enable-stream-vfd
-</pre>
-
-<UL>
-<li> --prefix=/usr/local/hdf5-mpich : the location where the HDF5 libs and
-binaries will be installed.</LI>
-<li> --enable-parallel : contrary to the HDF5 documentation, which says that
-"--enable-parallel" is optional for building the parallel version of
-HDF5, you <b>must</b> have --enable-parallel to get the parallel-enabled
-build. See <a href="ftp://ftp.hdfgroup.org/HDF5/current/src/unpacked/release_docs/INSTALL_parallel">these notes from HDF5</a> where they claim that
--enable-parallel is optional.</LI>
-<li> CC=mpicc CXX=mpicxx : contrary to the output from configure --help, the
-configure script seems to ignore the CC and CXX environment variables.
-We tried setting these environment variables to mpicc and mpicxx,
-respectively, and then ran configure with --enable-parallel. The configure
-script would faile with this error message: 	
-<pre>
-checking whether a simple MPI-IO program can be linked... no
-configure: error: unable to link a simple MPI-IO application
-</pre>
-</LI>
-<LI> --disable-shared and --enable-static: the HDF5 build failed for us
-w/o these options when attempting to read symbols from libmpich.a. The
-result of these options is that your parallel-enabled HDF5 libaries
-will be static rather than dynamic.
-
-</UL>
-
+	You will need to download and install the HDF5 library and link H5Part with it.
+	<UL>
+	  <LI><a href="ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.6.5.tar.gz">ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.6.5.tar.gz</a></LI>
+	  <LI><a href="http://www.zlib.net/zlib-1.2.3.tar.gz">http://www.zlib.net/zlib-1.2.3.tar.gz</a></LI>
+	  <LI><a href="ftp://ftp.hdfgroup.org/lib-external/szip/2.0/src/szip-2.0.tar.gz">ftp://ftp.hdfgroup.org/lib-external/szip/2.0/src/szib-2.0.tar.gz</a></LI>
+	</UL>
+         <P>
+	  Note: you might already have libz in your system and you will not need libsz unless you build hdf5 with support for it.
+         </P>

    <h2 id="h5part">Downloading H5Part</h2>
        H5Part is available for download from Berkeley Labs Codeforge system <a href="https://codeforge.lbl.gov/projects/h5part/">https://codeforge.lbl.gov/projects/h5part</a>.
@@ -4,7 +4,7 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 PROJECT_NAME           = H5Part
-PROJECT_NUMBER         = 1.3.1
+PROJECT_NUMBER         = 1.3.3
 OUTPUT_DIRECTORY       = ./ReferencePages
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English
@@ -6,8 +6,6 @@
 <meta name="keywords" content="scientific visualization">
 <meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">

-<!--#include virtual="/include/topIncludes.html"-->
-
 <div id="maincenter">


@@ -15,7 +13,7 @@
 	<title>H5Part Utility Tools</title>
 </head>

-  <body bgcolor="#F0F0F0">
+  <body>
    <font face="arial,helvetica" size="+2" color="#555588"><h2>H5Part Utility Tools</h2></font>
    <UL>
      <LI><a href="h5pAttrib">h5pAttrib</a>
@@ -94,6 +92,3 @@ usage: h5pToGNUplot -t TIMESTEP -1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTION

 </div>

-<!--#include virtual="/include/dateFooter.html"-->
-
-
@@ -0,0 +1,151 @@
+Proposal for a more general file format used by H5Part/H5Block
+
+                                                 Authors: Achim Gsell
+                                                 Status:  Draft
+
+1. Introduction
+
+H5X is the file format used by H5Part and H5Block.  H5X is designed on
+top of HDF5: A H5X file is a very special HDF5 file.
+
+	+--------------------+
+	|   Application      |
+	+--------------------+
+	| H5Part/H5Block API |
+	+--------------------+
+	|      H5X API       |
+	+--------------------+
+	|     HDF5 API       |
+	+--------------------+
+	|  Filesystem of OS  |
+	+--------------------+
+
+
+2. H5X file format specification
+
+2.1 The root group
+
+2.1.1 File attributes
+
+Attributes of the HDF5 root group are called "file attributes". There
+are no restrictions on file attribute names. Supported values are
+scalars and arrays of 64bit integer and 64bit floating point number as
+well as string values,  but not arrays of strings.
+
+2.1.1.1 Predefined file attributes
+
+__stepname__ (optional)
+	See below.
+
+__stepnumwidth__ (optional)
+	See below.
+
+2.1.2 Members of the root group
+
+Members of the root group are special formated HDF5 groups called
+"step groups".  The name of a step group is "<name>#<number>". 
+Whereby <name> is either defined by the optional file attribute
+__stepname__ or set to "Step" by default. <number> is an 
+unsigned integer less than 2^63. 
+
+/
+- Step#0
+- Step#1
+...
+- Step#n
+- StepProperties [NEW]
+- Mesh [NEW]
+
+The optional file attribute __stepnumwidth__ defines the minimum width
+of <number> in the name of the step group. The number is padded with
+'0'. The minimum width defaults to zero, so that no paddings occurs. 
+Example: With __stepnumwidth__ := 5 the name of the step group with
+number 42 is "Step#00042", with __stepnumwidth__ := 0 the name is
+"Step#42". 
+
+Step groups may be unsorted in the HDF5 file und may not be number
+consecutively. 
+
+
+2.2    Format of a step group
+
+2.2.1  Step attributes
+
+Step attributes are HDF5 attributes asigned to a step group.  There
+are no restrictions on file attribute names. Supported values are
+scalars and arrays of 64bit integer and 64bit floating point number as
+well as string values,  but not arrays of strings.
+
+2.2.2  Predefined step attributes
+
+No predefined step attributes exists.
+
+
+2.2.3  Members of a step group
+
+Members of a step group are HDF5 datasets and optional one HDF5 group
+with the name "Block". HDF5 datasets in a step group are called "step
+datasets". The optional block group is called "block data". 
+
+Mesh?!
+
+2.2.4  Step datasets
+
+Step datasets are arrays of rank 1.  The dataset size must be the same
+for all datasets inside a step.  The size of the dataset may vary
+from step to step.  Array values are 64bit integer or 64bit floating
+point numbers. No limitations (other than given by HDF5) are given on
+step dataset names.
+
+
+2.2.5  Block Data
+
+The block data group is a container for an arbitrary number of field
+data. A field is a data structure to store arrays of rank m with
+n-dimensional vector values. Fields are represented within HDF5
+groups. The HDF5 group name is the unique identifier for a field in
+the current step.
+
+2.2.5.1 m-rank fields with n-dimensional-vector values
+
+Values are stored per dimension in separate datasets. Thus we have n
+datasets for a field with n-dimensional vector values.  Each dataset
+corresponse to one dimension. The datasets are numbered from '0' to
+'n-1'. Arrays are stored in column major order (Fortran indexing
+scheme).
+
+/				# HDF5 root group
+...
+- Step#<i>			# HDF5 group
+   |
+   +- Block			# HDF5 group
+      |
+      +- <field name>		# HDF5 group
+         |
+         +- 0			# HDF5 dataset, first dim of vector
+	 +- 1			# HDF5 dataset, second dim of vector
+         ...
+        +- n-1			# HDF5 dataset, last dim of vector
+...
+
+2.2.5.2 m-rank fields with scalar values
+
+Fields with scalar values are stored as special case of fields with
+n-dimensional vector values with n := 1.
+
+/				# HDF5 root group
+...
+- Step#<i>			# HDF5 group
+   |
+   +- Block			# HDF5 group
+      |
+      +- <field name>		# HDF5 group
+         |
+         +- 0			# HDF5 dataset, scalar value
+...
+
+
+2.3    Step properties [NEW]
+
+
+
@@ -6,8 +6,6 @@
 <meta name="keywords" content="scientific visualization">
 <meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">

-<!--#include virtual="/include/topIncludes.html"-->
-
 <div id="maincenter">

 <h1>The C/C++ Application Programming Interface (API)</h1>
@@ -603,4 +601,3 @@ if (H5PartReadStepAttrib(file, "filename", &name[0]) == 1){

 </div>

-<!--#include virtual="/include/dateFooter.html"-->
@@ -6,8 +6,6 @@
 <meta name="keywords" content="scientific visualization">
 <meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">

-<!--#include virtual="/include/topIncludes.html"-->
-
 <div id="maincenter">


@@ -500,5 +498,3 @@ err=h5pt_readstepattrib(file,"RealTime",data)


 </div>
-
-<!--#include virtual="/include/dateFooter.html"-->
@@ -9,7 +9,7 @@

 <div id="maincenter">
 <font face="arial,helvetica"><h1>H5Part: a Portable High Performance Parallel Data Interface to HDF5</h1></font>
-<h2><font color="red"> THESE PAGES ARE UNDER CONSTRUCTION, September 2006</h2></font>
+<!--<h2><font color="red"> THESE PAGES ARE UNDER CONSTRUCTION, September 2006</h2></font>-->
 <font face="arial,helvetica" color="#555588"><h2>Motivation</h2></font>
 <P>
 <TABLE>
@@ -105,17 +105,17 @@ of datasets that contain multiple fields.
 <LI><a href="UsingF.html">Using the F77/F90 interface</a>
 <LI><a href="InternalLayout.html">Logical Internal HDF5 File</a>
 <LI><a href="H5PartTools.html">H5Part Utility Tools</a>
-<LI><a href="ReferencePages/index.html">Reference Manual</a>
+<LI><a href="ReferencePages/index.html">Reference Manual</a> (Note: Requires doxygen
+to be run in the directory /doc)
 </UL>

 <font face="arial,helvetica" color="#555588"><h2>H5Part Visualization Tools</h2></font>
 <UL>
-<LI><a href="H5PartExpress.html">H5Part Express Reader</a>
+<!--<LI><a href="H5PartExpress.html">H5Part Express Reader</a>-->
 <LI><a href="H5PartVisIt.html">H5Part VisIt Reader</a>
-<LI><a href="H5PartIDL.html">H5Part IDL Reader</a>
+<!--<LI><a href="H5PartIDL.html">H5Part IDL Reader</a>-->
 <LI><a href="http://www.cscs.ch/a-display.php?id=170">H5Part sparticles Reader: developed at CSCS, Switzerland</a>
-
-<LI><a href="H5PartPartView.html">PartView Visualization Application</a>
+<LI><a href="http://vis.lbl.gov/Vignettes/PartView/index.html">PartView Visualization Application</a>
 </UL>
 </div>

@@ -7,19 +7,40 @@ analysis needs to be preserved, reading and writing such enormous
 restart files on massively parallel supercomputing systems remains
 challenging. 

-H5Part consists of Particles, Block structured Fields and unstructured
-data (Topo).
+H5Part consists of Particles and Block structured Fields.

-Developed by  .
+Developed by:

-For further information contact: <a href="mailto:xxxxx">xxxxxx</a> - 
-xxxx xxxxx, (xxx) xxx.
+<UL>
+<LI> Andreas Adelmann (PSI) </LI>
+<LI> Achim Gsell (PSI) </LI>
+<LI> Benedikt Oswald (PSI) </LI>
+
+<LI> Wes Bethel (NERSC/LBNL)</LI>
+<LI> John Shalf (NERSC/LBNL)</LI>
+<LI> Cristina Siegerist (NERSC/LBNL)</LI>
+</UL>

-Last modified on xxx xx, 2006.

 Papers: 

-<a href="http://www-vis.lbl.gov/Research/AcceleratorSAPP/index.html">LBNL Vis Group </a><br>
+<UL>
+<LI> A. Adelmann, R.D. Ryne, C. Siegerist, J. Shalf,"From Visualization to Data Mining with Large Data Sets," <i>
+<a href="http://www.sns.gov/pac05">Particle Accelerator Conference (PAC05)</a></i>, Knoxville TN., May 16-20, 2005. (LBNL-57603)
+<a href="http://vis.lbl.gov/Publications/2005/FPAT082.pdf">FPAT082.pdf</a>
+</LI>
+
+
+<LI> A. Adelmann, R.D. Ryne, J. Shalf, C. Siegerist,"H5Part: A Portable High Performance Parallel Data Interface for Particle Simulations," <i>
+<a href="http://www.sns.gov/pac05">Particle Accelerator Conference (PAC05)</a></i>, Knoxville TN., May 16-20, 2005.
+<a href="http://vis.lbl.gov/Publications/2005/FPAT083.pdf">FPAT083.pdf</a>
+</LI>
+</UL>
+
+For further information contact: <a href="mailto:h5part@lists.psi.ch">h5part</a>
+
+Last modified on April 19, 2007.
+
 */


@@ -1601,7 +1622,8 @@ H5PartGetDatasetInfo (
 		f->groupname_step, f->stepno_width, (long long) f->timestep );

 	herr = _H5Part_get_object_name (
-		f->timegroup,
+					//f->timegroup,
+		f->file,
 		step_name,
 		H5G_DATASET,
 		idx,
@@ -22,13 +22,14 @@

 /*

-  bench <nParticles>
+bench <nParticles>


 */


 int main(int argc,char *argv[]){
+  printf("Start benchmarks...\n");
  MPI_Info info;
  int nprocs,rank;
  int trial;
@@ -48,6 +49,7 @@ int main(int argc,char *argv[]){
  H5PartFile *f;
 #endif
  char newfilename[128];
+  char lastfilename[128];
  FILE *fd;
  MPI_File file;
  MPI_Offset foffset;
@@ -74,7 +76,7 @@ int main(int argc,char *argv[]){

  
  /* printf("about to call create subarray with nparticles=%u localnp=%u offset=%u\n",
-	nparticles,localnp,offset); */
+     nparticles,localnp,offset); */
  MPI_Type_create_subarray(1, /* rank */
 			   &nparticles, /* size of the global array */
 			   &localnp, /* size of my local chunk */
@@ -86,148 +88,157 @@ int main(int argc,char *argv[]){
  MPI_Info_create(&info);

  if(rank==0) printf("Nprocs=%u Particles=%u*6attribs*sizeof(double) Particles/proc=%u Nsteps=%u Ntrials=%u\n",
-	nprocs,nparticles,localnp,NSTEPS,NTRIALS);
+		     nprocs,nparticles,localnp,NSTEPS,NTRIALS);
 	

  for(trial=0;trial<NTRIALS;trial++){
-  if(rank==0) printf("---------------------- Trial %u of %u ---------------------\n",trial+1,NTRIALS);
+    if(rank==0) printf("---------------------- Trial %u of %u ---------------------\n",trial+1,NTRIALS);


-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  sprintf(filename,"%s.%u.mpio.dat",FILENAME,nprocs);
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    sprintf(filename,"%s.%u.mpio.dat",FILENAME,nprocs);
+    sprintf(lastfilename,"%s.%u.mpio.dat",FILENAME,nprocs);

-  if(rank==0) unlink(filename);
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    if(rank==0) unlink(filename);
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */

-  MPI_File_open(MPI_COMM_WORLD,filename,
-	MPI_MODE_CREATE | MPI_MODE_RDWR,
-	info,&file);
+    MPI_File_open(MPI_COMM_WORLD,filename,
+		  MPI_MODE_CREATE | MPI_MODE_RDWR,
+		  info,&file);
 	
-  MPI_File_set_view(file,0,MPI_DOUBLE,chunktype,"native",info);
-  /* now a barrier to get the start timers roughly synced*/
-  MPI_Barrier(MPI_COMM_WORLD);
-  curtime = starttime = MPI_Wtime();
-  endtime = starttime+5.0*60.0; /* end in 5 minutes */
-  MPI_Bcast(&endtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
-  /* must touch the entire array after each write */
-  /* ensures cache-invalidation */
-  foffset=0;
-  i=0;
-  curtime=starttime;
-  for(i=0;i<NSTEPS;i++){
-    int n;
-    MPI_Status status;
-    for(j=0;j<6;j++){
-      /* touch data */
-      for(n=0;n<localnp;n++)
-	(data[j])[n]=(double)rank;
-      /* write to that file */
-      /*  MPI_File_set_view(file,foffset,MPI_DOUBLE,chunktype,"native",info);*/
-      MPI_File_write_at_all(file,
-			    foffset,
-			    data[j],
-			    localnp,
-			    MPI_DOUBLE,&status);
-      foffset+=nparticles/nprocs;
+    MPI_File_set_view(file,0,MPI_DOUBLE,chunktype,"native",info);
+    /* now a barrier to get the start timers roughly synced*/
+    MPI_Barrier(MPI_COMM_WORLD);
+    curtime = starttime = MPI_Wtime();
+    endtime = starttime+5.0*60.0; /* end in 5 minutes */
+    MPI_Bcast(&endtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
+    /* must touch the entire array after each write */
+    /* ensures cache-invalidation */
+    foffset=0;
+    i=0;
+    curtime=starttime;
+    for(i=0;i<NSTEPS;i++){
+      int n;
+      MPI_Status status;
+      for(j=0;j<6;j++){
+	/* touch data */
+	for(n=0;n<localnp;n++)
+	  (data[j])[n]=(double)rank;
+	/* write to that file */
+	/*  MPI_File_set_view(file,foffset,MPI_DOUBLE,chunktype,"native",info);*/
+	MPI_File_write_at_all(file,
+			      foffset,
+			      data[j],
+			      localnp,
+			      MPI_DOUBLE,&status);
+	foffset+=nparticles/nprocs;
+      }
+      curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
+      MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
+    }
+    MPI_File_close(&file);
+    MPI_Barrier(MPI_COMM_WORLD);
+    endtime=MPI_Wtime();
+    sprintf(filename,"%s.%u.h5.dat",FILENAME,nprocs);
+    /* foffset*=nprocs; if we want total megabytes written */
+    if(rank==0){
+      puts("*");
+      unlink(filename);
+      puts("======================================================");
+      printf("Raw MPI-IO Total Duration %lf seconds, iterations=%u %lf Megabytes written per processor Nprocs= %u \n",
+	     (endtime-starttime),i,((double)foffset)/(1024.0*1024.0),nprocs);
+      printf("Raw MPI-IO Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
+	     (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
+	     (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
+      puts("======================================================");
    }
-    curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
-    MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
-  }
-  MPI_File_close(&file);
-  MPI_Barrier(MPI_COMM_WORLD);
-  endtime=MPI_Wtime();
-  sprintf(filename,"%s.%u.h5.dat",FILENAME,nprocs);
-  /* foffset*=nprocs; if we want total megabytes written */
-  if(rank==0){
-    puts("*");
-    unlink(filename);
-    puts("======================================================");
-    printf("Raw MPI-IO Total Duration %lf seconds, iterations=%u %lf Megabytes written per processor Nprocs= %u \n",
-	   (endtime-starttime),i,((double)foffset)/(1024.0*1024.0),nprocs);
-    printf("Raw MPI-IO Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
-	   (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
-	   (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
-    puts("======================================================");
-  }

-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  /* OK, now we do this using H5Part */
-  sprintf(newfilename,"testio%u.%u.dat",rank,nprocs);
-  unlink(newfilename);
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  fd = fopen(newfilename,"w");
-  /* start the timer */
-  starttime=endtime=MPI_Wtime();
-  for(i=0;i<NSTEPS;i++){
-    for(j=0;j<6;j++){
-      /* touch data */
-      for(n=0;n<localnp;n++)
-	(data[j])[n]=(double)rank;
-      fwrite(data[j],sizeof(double),localnp,fd);
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    /* OK, now we do this using H5Part */
+    sprintf(newfilename,"testio%u.%u.dat",rank,nprocs);
+    unlink(newfilename);
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    fd = fopen(newfilename,"w");
+    /* start the timer */
+    starttime=endtime=MPI_Wtime();
+    for(i=0;i<NSTEPS;i++){
+      for(j=0;j<6;j++){
+	/* touch data */
+	for(n=0;n<localnp;n++)
+	  (data[j])[n]=(double)rank;
+	fwrite(data[j],sizeof(double),localnp,fd);
+      }
+      curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
+      MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
+    }
+    fclose(fd);
+    MPI_Barrier(MPI_COMM_WORLD);
+    endtime=MPI_Wtime();
+    if(rank==0) puts("*");
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    unlink(newfilename);
+    MPI_Barrier(MPI_COMM_WORLD);
+    if(rank==0){
+      puts("======================================================");
+      printf("Raw 1-file-per-proc Total Duration %lf seconds, iterations=%u %lf Megabytes written Nprocs= %u \n",
+	     (endtime-starttime),NSTEPS,((double)foffset)/(1024.0*1024.0),nprocs);
+      printf("Raw 1-file-per-proc Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
+	     (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
+	     (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
+      puts("======================================================");
    }
-    curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
-    MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
-  }
-  fclose(fd);
-  MPI_Barrier(MPI_COMM_WORLD);
-  endtime=MPI_Wtime();
-  if(rank==0) puts("*");
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  unlink(newfilename);
-  MPI_Barrier(MPI_COMM_WORLD);
-  if(rank==0){
-    puts("======================================================");
-    printf("Raw 1-file-per-proc Total Duration %lf seconds, iterations=%u %lf Megabytes written Nprocs= %u \n",
-	   (endtime-starttime),NSTEPS,((double)foffset)/(1024.0*1024.0),nprocs);
-    printf("Raw 1-file-per-proc Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
-	   (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
-	   (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
-    puts("======================================================");
-  }

 #ifndef DISABLE_H5PART
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  /* OK, now we do this using H5Part */
-  f = H5PartOpenFileParallel(filename,H5PART_WRITE,MPI_COMM_WORLD);
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  /* start the timer */
-  starttime=endtime=MPI_Wtime();
-  H5PartSetNumParticles(f,localnp);
-  for(i=0;i<NSTEPS;i++){
-    for(j=0;j<6;j++){
-      /* touch data */
-      for(n=0;n<localnp;n++)
-	(data[j])[n]=(double)rank;
-    }
-    H5PartSetStep(f,i);
-    H5PartWriteDataFloat64(f,"x",x);
-    H5PartWriteDataFloat64(f,"y",y);
-    H5PartWriteDataFloat64(f,"z",z);
-    H5PartWriteDataFloat64(f,"px",px);
-    H5PartWriteDataFloat64(f,"py",py);
-    H5PartWriteDataFloat64(f,"pz",pz);
+    //printf("H5Part benchmark...");
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    /* OK, now we do this using H5Part */
+    f = H5PartOpenFileParallel(filename,H5PART_WRITE,MPI_COMM_WORLD);
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    /* start the timer */
+    starttime=endtime=MPI_Wtime();
+    H5PartSetNumParticles(f,localnp);
+    for(i=0;i<NSTEPS;i++){
+      for(j=0;j<6;j++){
+	/* touch data */
+	for(n=0;n<localnp;n++)
+	  (data[j])[n]=(double)rank;
+      }
+      H5PartSetStep(f,i);
+      H5PartWriteDataFloat64(f,"x",x);
+      H5PartWriteDataFloat64(f,"y",y);
+      H5PartWriteDataFloat64(f,"z",z);
+      H5PartWriteDataFloat64(f,"px",px);
+      H5PartWriteDataFloat64(f,"py",py);
+      H5PartWriteDataFloat64(f,"pz",pz);

-    curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
-    MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
-  }
-  H5PartCloseFile(f);
-  MPI_Barrier(MPI_COMM_WORLD);
-  endtime=MPI_Wtime();
-  if(rank==0){
-    puts("*");
-    unlink(filename);
-    puts("======================================================");
-    printf("H5Part Total Duration %lf seconds, iterations=%u %lf Megabytes written Nprocs= %u \n",
-	   (endtime-starttime),NSTEPS,((double)foffset)/(1024.0*1024.0),nprocs);
-    printf("H5Part Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
-	   (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
-	   (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
-    puts("======================================================");
-  }
-  MPI_Barrier(MPI_COMM_WORLD);
+      curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
+      MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
+    }
+    H5PartCloseFile(f);
+    MPI_Barrier(MPI_COMM_WORLD);
+    endtime=MPI_Wtime();
+    if(rank==0){
+      puts("*");
+      unlink(filename);
+      puts("======================================================");
+      printf("H5Part Total Duration %lf seconds, iterations=%u %lf Megabytes written Nprocs= %u \n",
+	     (endtime-starttime),NSTEPS,((double)foffset)/(1024.0*1024.0),nprocs);
+      printf("H5Part Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
+	     (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
+	     (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
+      puts("======================================================");
+    }
+    MPI_Barrier(MPI_COMM_WORLD);
 #endif
  } /* trials */
+
+  if (rank==0) {
+    printf("lastfilename: %s \n", lastfilename);
+    unlink(lastfilename);
+  }
+
  MPI_Finalize();

+
  return 0;
 }
Author	SHA1	Message	Date
Kurt Stockinger	7d140c6cb6	Preparing tag 1.4	2007-08-29 01:43:58 +00:00
gsell	8d760dc264	configure.ac: incr version number to 1.3.3 and bug-report address changed	2007-04-25 07:21:56 +00:00
Kurt Stockinger	4546846f06	Delete all files are benchmark is done.	2007-04-24 22:48:53 +00:00
Kurt Stockinger	62c46dc8bf	Minor documentation updates.	2007-04-24 21:57:28 +00:00
gsell	9516e493bc	doc/Downloading - fix links to software - HDF5 build instructions removed	2007-04-20 12:00:40 +00:00
gsell	9df1d56714	doc/BuildingHDF5.html - SSI statements removed - bgcolor removed	2007-04-20 11:59:54 +00:00
gsell	98e1055b7b	doc/UsingC.html doc/UsingF.html - SSI statements removed	2007-04-20 11:58:58 +00:00
gsell	436cce16c7	doc/H5PartTools.html - SSI statements removed - bgcolor removed	2007-04-20 11:57:57 +00:00
gsell	ec6f30bbd8	- doc/H5X_File_Format.txt * added	2007-04-20 08:33:47 +00:00
Kurt Stockinger	d356142bc4	Commented out some dead links.	2007-04-19 22:06:53 +00:00
Kurt Stockinger	00c9b0804b	Updated doxygen information.	2007-04-19 21:43:57 +00:00