summaryrefslogtreecommitdiff
path: root/src/tests
diff options
context:
space:
mode:
Diffstat (limited to 'src/tests')
-rw-r--r--src/tests/compression/testsuite.c434
-rw-r--r--src/tests/tng_io_testing.c38
-rw-r--r--src/tests/tng_parallel_read.c56
3 files changed, 309 insertions, 219 deletions
diff --git a/src/tests/compression/testsuite.c b/src/tests/compression/testsuite.c
index 27450d6..73ade62 100644
--- a/src/tests/compression/testsuite.c
+++ b/src/tests/compression/testsuite.c
@@ -78,20 +78,20 @@ static int intcos(int i)
}
static void molecule(int *target,
- int *base,
- int length,
- int scale, int *direction,
- int flip,
- int iframe)
+ int *base,
+ int length,
+ int scale, int *direction,
+ int flip,
+ int iframe)
{
int i;
for (i=0; i<length; i++)
{
int ifl=i;
if ((i==0) && (flip) && (length>1))
- ifl=1;
+ ifl=1;
else if ((i==1) && (flip) && (length>1))
- ifl=0;
+ ifl=0;
target[ifl*3]=base[0]+(intsin((i+iframe)*direction[0])*scale)/256;
target[ifl*3+1]=base[1]+(intcos((i+iframe)*direction[1])*scale)/256;
target[ifl*3+2]=base[2]+(intcos((i+iframe)*direction[2])*scale)/256;
@@ -125,40 +125,40 @@ static void genibox(int *intbox, int iframe)
scale=1;
#endif
if (i+this_mol_length>NATOMS)
- this_mol_length=NATOMS-i;
+ this_mol_length=NATOMS-i;
/* We must test the large rle as well. This requires special
- sequencies to get triggered. So insert these from time to
- time */
+ sequencies to get triggered. So insert these from time to
+ time */
#ifndef REGULAR
if ((i%10)==0)
- {
- int j;
- intbox[i*3]=molpos[0];
- intbox[i*3+1]=molpos[1];
- intbox[i*3+2]=molpos[2];
- for (j=1; j<this_mol_length; j++)
- {
- intbox[(i+j)*3]=intbox[(i+j-1)*3]+(INTMAX1-INTMIN1+1)/5;
- intbox[(i+j)*3+1]=intbox[(i+j-1)*3+1]+(INTMAX2-INTMIN2+1)/5;
- intbox[(i+j)*3+2]=intbox[(i+j-1)*3+2]+(INTMAX3-INTMIN3+1)/5;
- keepinbox(intbox+(i+j)*3);
- }
- }
+ {
+ int j;
+ intbox[i*3]=molpos[0];
+ intbox[i*3+1]=molpos[1];
+ intbox[i*3+2]=molpos[2];
+ for (j=1; j<this_mol_length; j++)
+ {
+ intbox[(i+j)*3]=intbox[(i+j-1)*3]+(INTMAX1-INTMIN1+1)/5;
+ intbox[(i+j)*3+1]=intbox[(i+j-1)*3+1]+(INTMAX2-INTMIN2+1)/5;
+ intbox[(i+j)*3+2]=intbox[(i+j-1)*3+2]+(INTMAX3-INTMIN3+1)/5;
+ keepinbox(intbox+(i+j)*3);
+ }
+ }
else
#endif
- molecule(intbox+i*3,molpos,this_mol_length,scale,direction,flip,iframe*FRAMESCALE);
+ molecule(intbox+i*3,molpos,this_mol_length,scale,direction,flip,iframe*FRAMESCALE);
i+=this_mol_length;
dir=1;
if (intsin(i*3)<0)
- dir=-1;
+ dir=-1;
molpos[0]+=dir*(INTMAX1-INTMIN1+1)/20;
dir=1;
if (intsin(i*5)<0)
- dir=-1;
+ dir=-1;
molpos[1]+=dir*(INTMAX2-INTMIN2+1)/20;
dir=1;
if (intsin(i*7)<0)
- dir=-1;
+ dir=-1;
molpos[2]+=dir*(INTMAX3-INTMIN3+1)/20;
keepinbox(molpos);
@@ -168,13 +168,13 @@ static void genibox(int *intbox, int iframe)
scale++;
if (scale>5)
- scale=1;
+ scale=1;
molecule_length++;
if (molecule_length>30)
- molecule_length=1;
+ molecule_length=1;
if (i%9)
- flip=1-flip;
+ flip=1-flip;
}
}
@@ -217,9 +217,9 @@ static void realbox(int *intbox, REAL *realbox, int stride)
for (i=0; i<NATOMS; i++)
{
for (j=0; j<3; j++)
- realbox[i*stride+j]=(REAL)(intbox[i*3+j]*GENPRECISION*SCALE);
+ realbox[i*stride+j]=(REAL)(intbox[i*3+j]*GENPRECISION*SCALE);
for (j=3; j<stride; j++)
- realbox[i*stride+j]=0.;
+ realbox[i*stride+j]=0.;
}
}
@@ -229,9 +229,9 @@ static void realvelbox(int *intbox, REAL *realbox, int stride)
for (i=0; i<NATOMS; i++)
{
for (j=0; j<3; j++)
- realbox[i*stride+j]=(REAL)(intbox[i*3+j]*GENVELPRECISION*SCALE);
+ realbox[i*stride+j]=(REAL)(intbox[i*3+j]*GENVELPRECISION*SCALE);
for (j=3; j<stride; j++)
- realbox[i*stride+j]=0.;
+ realbox[i*stride+j]=0.;
}
}
@@ -242,14 +242,14 @@ static int equalarr(REAL *arr1, REAL *arr2, REAL prec, int len, int itemlen, int
for (i=0; i<len; i++)
{
for (j=0; j<itemlen; j++)
- if (fabs(arr1[i*stride1+j]-arr2[i*stride2+j])>maxdiff)
- maxdiff=(REAL)fabs(arr1[i*stride1+j]-arr2[i*stride2+j]);
+ if (fabs(arr1[i*stride1+j]-arr2[i*stride2+j])>maxdiff)
+ maxdiff=(REAL)fabs(arr1[i*stride1+j]-arr2[i*stride2+j]);
}
#if 0
for (i=0; i<len; i++)
{
for (j=0; j<itemlen; j++)
- printf("%d %d: %g %g\n",i,j,arr1[i*stride1+j],arr2[i*stride2+j]);
+ printf("%d %d: %g %g\n",i,j,arr1[i*stride1+j],arr2[i*stride2+j]);
}
#endif
#if 0
@@ -315,19 +315,19 @@ static size_t fread_int_le(int *x,FILE *f)
}
static struct tng_file *open_tng_file_write(char *filename,
- int natoms,int chunky,
- REAL precision,
- int writevel,
- REAL velprecision,
- int initial_coding,
- int initial_coding_parameter,
- int coding,
- int coding_parameter,
- int initial_velcoding,
- int initial_velcoding_parameter,
- int velcoding,
- int velcoding_parameter,
- int speed)
+ int natoms,int chunky,
+ REAL precision,
+ int writevel,
+ REAL velprecision,
+ int initial_coding,
+ int initial_coding_parameter,
+ int coding,
+ int coding_parameter,
+ int initial_velcoding,
+ int initial_velcoding_parameter,
+ int velcoding,
+ int velcoding_parameter,
+ int speed)
{
struct tng_file *tng_file=malloc(sizeof *tng_file);
tng_file->pos=NULL;
@@ -358,17 +358,17 @@ static struct tng_file *open_tng_file_write(char *filename,
}
static struct tng_file *open_tng_file_write_int(char *filename,
- int natoms,int chunky,
- int writevel,
- int initial_coding,
- int initial_coding_parameter,
- int coding,
- int coding_parameter,
- int initial_velcoding,
- int initial_velcoding_parameter,
- int velcoding,
- int velcoding_parameter,
- int speed)
+ int natoms,int chunky,
+ int writevel,
+ int initial_coding,
+ int initial_coding_parameter,
+ int coding,
+ int coding_parameter,
+ int initial_velcoding,
+ int initial_velcoding_parameter,
+ int velcoding,
+ int velcoding_parameter,
+ int speed)
{
struct tng_file *tng_file=malloc(sizeof *tng_file);
tng_file->pos=NULL;
@@ -397,8 +397,8 @@ static struct tng_file *open_tng_file_write_int(char *filename,
}
static void flush_tng_frames(struct tng_file *tng_file,
- unsigned long prec_hi, unsigned long prec_lo,
- unsigned long velprec_hi, unsigned long velprec_lo)
+ unsigned long prec_hi, unsigned long prec_lo,
+ unsigned long velprec_hi, unsigned long velprec_lo)
{
int algo[4];
char *buf;
@@ -410,23 +410,23 @@ static void flush_tng_frames(struct tng_file *tng_file,
algo[3]=tng_file->coding_parameter;
#ifdef RECOMPRESS
buf=tng_compress_pos_int(tng_file->ipos,
- tng_file->natoms,
- tng_file->nframes,
- prec_hi,prec_lo,
- tng_file->speed,algo,&nitems);
+ tng_file->natoms,
+ tng_file->nframes,
+ prec_hi,prec_lo,
+ tng_file->speed,algo,&nitems);
#else /* RECOMPRESS */
#ifdef TEST_FLOAT
buf=tng_compress_pos_float(tng_file->pos,
- tng_file->natoms,
- tng_file->nframes,
- tng_file->precision,
- tng_file->speed,algo,&nitems);
+ tng_file->natoms,
+ tng_file->nframes,
+ tng_file->precision,
+ tng_file->speed,algo,&nitems);
#else /* TEST_FLOAT */
buf=tng_compress_pos(tng_file->pos,
- tng_file->natoms,
- tng_file->nframes,
- tng_file->precision,
- tng_file->speed,algo,&nitems);
+ tng_file->natoms,
+ tng_file->nframes,
+ tng_file->precision,
+ tng_file->speed,algo,&nitems);
#endif /* TEST_FLOAT */
#endif /* RECOMPRESS */
tng_file->initial_coding=algo[0];
@@ -444,23 +444,23 @@ static void flush_tng_frames(struct tng_file *tng_file,
algo[3]=tng_file->velcoding_parameter;
#ifdef RECOMPRESS
buf=tng_compress_vel_int(tng_file->ivel,
- tng_file->natoms,
- tng_file->nframes,
- velprec_hi,velprec_lo,
- tng_file->speed,algo,&nitems);
+ tng_file->natoms,
+ tng_file->nframes,
+ velprec_hi,velprec_lo,
+ tng_file->speed,algo,&nitems);
#else /* RECOMPRESS */
#ifdef TEST_FLOAT
buf=tng_compress_vel_float(tng_file->vel,
- tng_file->natoms,
- tng_file->nframes,
- tng_file->velprecision,
- tng_file->speed,algo,&nitems);
+ tng_file->natoms,
+ tng_file->nframes,
+ tng_file->velprecision,
+ tng_file->speed,algo,&nitems);
#else /* TEST_FLOAT */
buf=tng_compress_vel(tng_file->vel,
- tng_file->natoms,
- tng_file->nframes,
- tng_file->velprecision,
- tng_file->speed,algo,&nitems);
+ tng_file->natoms,
+ tng_file->nframes,
+ tng_file->velprecision,
+ tng_file->speed,algo,&nitems);
#endif /* TEST_FLOAT */
#endif /* RECOMPRESS */
tng_file->initial_velcoding=algo[0];
@@ -475,7 +475,7 @@ static void flush_tng_frames(struct tng_file *tng_file,
}
static void write_tng_file(struct tng_file *tng_file,
- REAL *pos,REAL *vel)
+ REAL *pos,REAL *vel)
{
memcpy(tng_file->pos+tng_file->nframes*tng_file->natoms*3,pos,tng_file->natoms*3*sizeof *tng_file->pos);
if (tng_file->writevel)
@@ -486,9 +486,9 @@ static void write_tng_file(struct tng_file *tng_file,
}
static void write_tng_file_int(struct tng_file *tng_file,
- int *ipos,int *ivel,
- unsigned long prec_hi, unsigned long prec_lo,
- unsigned long velprec_hi, unsigned long velprec_lo)
+ int *ipos,int *ivel,
+ unsigned long prec_hi, unsigned long prec_lo,
+ unsigned long velprec_hi, unsigned long velprec_lo)
{
memcpy(tng_file->ipos+tng_file->nframes*tng_file->natoms*3,ipos,tng_file->natoms*3*sizeof *tng_file->ipos);
if (tng_file->writevel)
@@ -557,8 +557,8 @@ static struct tng_file *open_tng_file_read_int(char *filename, int writevel)
}
static int read_tng_file(struct tng_file *tng_file,
- REAL *pos,
- REAL *vel)
+ REAL *pos,
+ REAL *vel)
{
if (tng_file->nframes==tng_file->nframes_delivered)
{
@@ -567,25 +567,28 @@ static int read_tng_file(struct tng_file *tng_file,
free(tng_file->pos);
free(tng_file->vel);
if (!fread_int_le(&tng_file->nframes,tng_file->f))
- return 1;
+ return 1;
if (!fread_int_le(&nitems,tng_file->f))
- return 1;
+ return 1;
buf=malloc(nitems);
if (!fread(buf,1,nitems,tng_file->f))
- return 1;
+ {
+ free(buf);
+ return 1;
+ }
tng_file->pos=malloc(tng_file->natoms*tng_file->nframes*3*sizeof *tng_file->pos);
if (tng_file->writevel)
- tng_file->vel=malloc(tng_file->natoms*tng_file->nframes*3*sizeof *tng_file->vel);
+ tng_file->vel=malloc(tng_file->natoms*tng_file->nframes*3*sizeof *tng_file->vel);
#if 0
{
- int natoms, nframes, algo[4];
- double precision;
- int ivel;
- char *initial_coding, *coding;
- tng_compress_inquire(buf,&ivel,&natoms,&nframes,&precision,algo);
- initial_coding=tng_compress_initial_pos_algo(algo);
- coding=tng_compress_pos_algo(algo);
- printf("ivel=%d natoms=%d nframes=%d precision=%g initial pos=%s pos=%s\n",ivel,natoms,nframes,precision,initial_coding,coding);
+ int natoms, nframes, algo[4];
+ double precision;
+ int ivel;
+ char *initial_coding, *coding;
+ tng_compress_inquire(buf,&ivel,&natoms,&nframes,&precision,algo);
+ initial_coding=tng_compress_initial_pos_algo(algo);
+ coding=tng_compress_pos_algo(algo);
+ printf("ivel=%d natoms=%d nframes=%d precision=%g initial pos=%s pos=%s\n",ivel,natoms,nframes,precision,initial_coding,coding);
}
#endif
#ifdef TEST_FLOAT
@@ -595,31 +598,34 @@ static int read_tng_file(struct tng_file *tng_file,
#endif
free(buf);
if (tng_file->writevel)
- {
- if (!fread_int_le(&nitems,tng_file->f))
- return 1;
- buf=malloc(nitems);
- if (!fread(buf,1,nitems,tng_file->f))
- return 1;
+ {
+ if (!fread_int_le(&nitems,tng_file->f))
+ return 1;
+ buf=malloc(nitems);
+ if (!fread(buf,1,nitems,tng_file->f))
+ {
+ free(buf);
+ return 1;
+ }
#if 0
- {
- int natoms, nframes, algo[4];
- double precision;
- int ivel;
- char *initial_coding, *coding;
- tng_compress_inquire(buf,&ivel,&natoms,&nframes,&precision,algo);
- initial_coding=tng_compress_initial_vel_algo(algo);
- coding=tng_compress_vel_algo(algo);
- printf("ivel=%d natoms=%d nframes=%d precision=%g initial vel=%s vel=%s\n",ivel,natoms,nframes,precision,initial_coding,coding);
- }
+ {
+ int natoms, nframes, algo[4];
+ double precision;
+ int ivel;
+ char *initial_coding, *coding;
+ tng_compress_inquire(buf,&ivel,&natoms,&nframes,&precision,algo);
+ initial_coding=tng_compress_initial_vel_algo(algo);
+ coding=tng_compress_vel_algo(algo);
+ printf("ivel=%d natoms=%d nframes=%d precision=%g initial vel=%s vel=%s\n",ivel,natoms,nframes,precision,initial_coding,coding);
+ }
#endif
#ifdef TEST_FLOAT
- tng_compress_uncompress_float(buf,tng_file->vel);
+ tng_compress_uncompress_float(buf,tng_file->vel);
#else
- tng_compress_uncompress(buf,tng_file->vel);
+ tng_compress_uncompress(buf,tng_file->vel);
#endif
- free(buf);
- }
+ free(buf);
+ }
tng_file->nframes_delivered=0;
}
memcpy(pos,tng_file->pos+tng_file->nframes_delivered*tng_file->natoms*3,tng_file->natoms*3*sizeof *pos);
@@ -630,10 +636,10 @@ static int read_tng_file(struct tng_file *tng_file,
}
static int read_tng_file_int(struct tng_file *tng_file,
- int *ipos,
- int *ivel,
- unsigned long *prec_hi, unsigned long *prec_lo,
- unsigned long *velprec_hi, unsigned long *velprec_lo)
+ int *ipos,
+ int *ivel,
+ unsigned long *prec_hi, unsigned long *prec_lo,
+ unsigned long *velprec_hi, unsigned long *velprec_lo)
{
if (tng_file->nframes==tng_file->nframes_delivered)
{
@@ -642,27 +648,33 @@ static int read_tng_file_int(struct tng_file *tng_file,
free(tng_file->ipos);
free(tng_file->ivel);
if (!fread_int_le(&tng_file->nframes,tng_file->f))
- return 1;
+ return 1;
if (!fread_int_le(&nitems,tng_file->f))
- return 1;
+ return 1;
buf=malloc(nitems);
if (!fread(buf,1,nitems,tng_file->f))
- return 1;
+ {
+ free(buf);
+ return 1;
+ }
tng_file->ipos=malloc(tng_file->natoms*tng_file->nframes*3*sizeof *tng_file->ipos);
if (tng_file->writevel)
- tng_file->ivel=malloc(tng_file->natoms*tng_file->nframes*3*sizeof *tng_file->ivel);
+ tng_file->ivel=malloc(tng_file->natoms*tng_file->nframes*3*sizeof *tng_file->ivel);
tng_compress_uncompress_int(buf,tng_file->ipos,prec_hi,prec_lo);
free(buf);
if (tng_file->writevel)
- {
- if (!fread_int_le(&nitems,tng_file->f))
- return 1;
- buf=malloc(nitems);
- if (!fread(buf,1,nitems,tng_file->f))
- return 1;
- tng_compress_uncompress_int(buf,tng_file->ivel,velprec_hi,velprec_lo);
- free(buf);
- }
+ {
+ if (!fread_int_le(&nitems,tng_file->f))
+ return 1;
+ buf=malloc(nitems);
+ if (!fread(buf,1,nitems,tng_file->f))
+ {
+ free(buf);
+ return 1;
+ }
+ tng_compress_uncompress_int(buf,tng_file->ivel,velprec_hi,velprec_lo);
+ free(buf);
+ }
tng_file->nframes_delivered=0;
}
memcpy(ipos,tng_file->ipos+tng_file->nframes_delivered*tng_file->natoms*3,tng_file->natoms*3*sizeof *ipos);
@@ -682,7 +694,7 @@ static void close_tng_file_read(struct tng_file *tng_file)
free(tng_file);
}
-
+
#ifndef EXPECTED_FILESIZE
#define EXPECTED_FILESIZE 1
@@ -724,6 +736,8 @@ static int algotest()
#ifdef GEN
FILE *file;
REAL filesize;
+ REAL *box2=0;
+ REAL *velbox2=0;
#else
int i2;
int readreturn;
@@ -734,28 +748,48 @@ static int algotest()
#endif
#ifdef RECOMPRESS
void *dumpfile=open_tng_file_write_int(TNG_COMPRESS_FILES_DIR FILENAME,NATOMS,CHUNKY,
- WRITEVEL,
- INITIALCODING,
- INITIALCODINGPARAMETER,CODING,CODINGPARAMETER,
- INITIALVELCODING,INITIALVELCODINGPARAMETER,
- VELCODING,VELCODINGPARAMETER,SPEED);
+ WRITEVEL,
+ INITIALCODING,
+ INITIALCODINGPARAMETER,CODING,CODINGPARAMETER,
+ INITIALVELCODING,INITIALVELCODINGPARAMETER,
+ VELCODING,VELCODINGPARAMETER,SPEED);
void *dumpfile_recompress=open_tng_file_read_int(TNG_COMPRESS_FILES_DIR RECOMPRESS,WRITEVEL);
if (!dumpfile_recompress)
- return 1;
+ {
+ free(intbox);
+ free(intvelbox);
+ free(box1);
+ free(velbox1);
+ if(box2)
+ free(box2);
+ if(velbox2)
+ free(velbox2);
+ return 1;
+ }
#else /* RECOMPRESS */
#ifdef GEN
void *dumpfile=open_tng_file_write(TNG_COMPRESS_FILES_DIR FILENAME,NATOMS,CHUNKY,
- PRECISION,WRITEVEL,VELPRECISION,
- INITIALCODING,
- INITIALCODINGPARAMETER,CODING,CODINGPARAMETER,
- INITIALVELCODING,INITIALVELCODINGPARAMETER,
- VELCODING,VELCODINGPARAMETER,SPEED);
+ PRECISION,WRITEVEL,VELPRECISION,
+ INITIALCODING,
+ INITIALCODINGPARAMETER,CODING,CODINGPARAMETER,
+ INITIALVELCODING,INITIALVELCODINGPARAMETER,
+ VELCODING,VELCODINGPARAMETER,SPEED);
#else
void *dumpfile=open_tng_file_read(TNG_COMPRESS_FILES_DIR FILENAME,WRITEVEL);
#endif
#endif /* RECOMPRESS */
if (!dumpfile)
- return 1;
+ {
+ free(intbox);
+ free(intvelbox);
+ free(box1);
+ free(velbox1);
+ if(box2)
+ free(box2);
+ if(velbox2)
+ free(velbox2);
+ return 1;
+ }
for (i=0; i<9; i++)
H1[i]=0.;
H1[0]=INTMAX1*PRECISION*SCALE;
@@ -767,7 +801,7 @@ static int algotest()
unsigned long prec_hi, prec_lo;
unsigned long velprec_hi, velprec_lo;
if (read_tng_file_int(dumpfile_recompress,intbox,intvelbox,&prec_hi,&prec_lo,&velprec_hi,&velprec_lo))
- return 1;
+ return 1;
write_tng_file_int(dumpfile,intbox,intvelbox,prec_hi,prec_lo,velprec_hi,velprec_lo);
#else /* RECOMPRESS */
genibox(intbox,i);
@@ -783,45 +817,75 @@ static int algotest()
#else /* GEN */
#ifdef INTTOFLOAT
{
- unsigned long prec_hi, prec_lo;
- unsigned long velprec_hi, velprec_lo;
- readreturn=read_tng_file_int(dumpfile,intbox,intvelbox,&prec_hi,&prec_lo,&velprec_hi,&velprec_lo);
- if (!readreturn)
- {
- tng_compress_int_to_float(intbox,prec_hi,prec_lo,NATOMS,1,box2);
+ unsigned long prec_hi, prec_lo;
+ unsigned long velprec_hi, velprec_lo;
+ readreturn=read_tng_file_int(dumpfile,intbox,intvelbox,&prec_hi,&prec_lo,&velprec_hi,&velprec_lo);
+ if (!readreturn)
+ {
+ tng_compress_int_to_float(intbox,prec_hi,prec_lo,NATOMS,1,box2);
#if WRITEVEL
- tng_compress_int_to_float(intvelbox,velprec_hi,velprec_lo,NATOMS,1,velbox2);
+ tng_compress_int_to_float(intvelbox,velprec_hi,velprec_lo,NATOMS,1,velbox2);
#endif
- }
+ }
}
#else /* INTTOFLOAT */
#ifdef INTTODOUBLE
{
- unsigned long prec_hi, prec_lo;
- unsigned long velprec_hi, velprec_lo;
- readreturn=read_tng_file_int(dumpfile,intbox,intvelbox,&prec_hi,&prec_lo,&velprec_hi,&velprec_lo);
- if (!readreturn)
- {
- tng_compress_int_to_double(intbox,prec_hi,prec_lo,NATOMS,1,box2);
+ unsigned long prec_hi, prec_lo;
+ unsigned long velprec_hi, velprec_lo;
+ readreturn=read_tng_file_int(dumpfile,intbox,intvelbox,&prec_hi,&prec_lo,&velprec_hi,&velprec_lo);
+ if (!readreturn)
+ {
+ tng_compress_int_to_double(intbox,prec_hi,prec_lo,NATOMS,1,box2);
#if WRITEVEL
- tng_compress_int_to_double(intvelbox,velprec_hi,velprec_lo,NATOMS,1,velbox2);
+ tng_compress_int_to_double(intvelbox,velprec_hi,velprec_lo,NATOMS,1,velbox2);
#endif
- }
+ }
}
#else /* INTTODOUBLE */
readreturn=read_tng_file(dumpfile,box2,velbox2);
#endif /* INTTODOUBLE */
#endif /* INTTOFLOAT */
if (readreturn==1) /* general read error */
- return 1;
+ {
+ free(intbox);
+ free(intvelbox);
+ free(box1);
+ free(velbox1);
+ if(box2)
+ free(box2);
+ if(velbox2)
+ free(velbox2);
+ return 1;
+ }
#endif /* GEN */
#ifndef GEN
/* Check for equality of boxes. */
if (!equalarr(box1,box2,(REAL)PRECISION,NATOMS,3,STRIDE1,STRIDE2))
- return 4;
+ {
+ free(intbox);
+ free(intvelbox);
+ free(box1);
+ free(velbox1);
+ if(box2)
+ free(box2);
+ if(velbox2)
+ free(velbox2);
+ return 4;
+ }
#if WRITEVEL
if (!equalarr(velbox1,velbox2,(REAL)VELPRECISION,NATOMS,3,STRIDE1,STRIDE2))
- return 5;
+ {
+ free(intbox);
+ free(intvelbox);
+ free(box1);
+ free(velbox1);
+ if(box2)
+ free(box2);
+ if(velbox2)
+ free(velbox2);
+ return 5;
+ }
#endif
#endif /* GEN */
#endif /* RECOMPRESS */
@@ -846,16 +910,32 @@ static int algotest()
{
char b;
if (!fread(&b,1,1,file))
- break;
+ break;
filesize++;
}
fclose(file);
if (filesize>0)
{
if ((fabs(filesize-EXPECTED_FILESIZE)/EXPECTED_FILESIZE)>0.05)
- return 9;
+ {
+ free(intvelbox);
+ free(box1);
+ free(velbox1);
+ if(box2)
+ free(box2);
+ if(velbox2)
+ free(velbox2);
+ return 9;
+ }
}
#endif
+ free(intvelbox);
+ free(box1);
+ free(velbox1);
+ if(box2)
+ free(box2);
+ if(velbox2)
+ free(velbox2);
return 0;
}
diff --git a/src/tests/tng_io_testing.c b/src/tests/tng_io_testing.c
index 96b53f7..0f67ccc 100644
--- a/src/tests/tng_io_testing.c
+++ b/src/tests/tng_io_testing.c
@@ -136,7 +136,7 @@ static tng_function_status tng_test_read_and_write_file
}
stat = tng_frame_set_write(traj, TNG_USE_HASH);
}
-
+
return(stat);
}
@@ -148,11 +148,11 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj)
int64_t frame_nr;
double box_shape[9];
char atom_type[16], annotation[128];
- tng_function_status stat;
+ tng_function_status stat = TNG_SUCCESS;
tng_medium_stride_length_set(traj, 10);
tng_long_stride_length_set(traj, 100);
-
+
/* Create molecules */
if(tng_test_setup_molecules(traj) == TNG_CRITICAL)
{
@@ -200,7 +200,7 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj)
printf("Failed setting partial charges.\n");
return(TNG_CRITICAL);
}
-
+
stat = tng_particle_data_block_add(traj, TNG_TRAJ_PARTIAL_CHARGES, "PARTIAL CHARGES",
TNG_FLOAT_DATA, TNG_NON_TRAJECTORY_BLOCK,
1, 1, 1, 0, n_particles,
@@ -230,9 +230,9 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj)
printf("Cannot write file headers.\n");
}
-
+
tng_num_frames_per_frame_set_get(traj, &n_frames_per_frame_set);
-
+
data = malloc(sizeof(float) * n_particles *
n_frames_per_frame_set * 3);
if(!data)
@@ -366,9 +366,9 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj)
return(TNG_CRITICAL);
}
}
-
+
/* Write two more frame sets one frame at a time */
- cnt = 0;
+
/* Make a new frame set - if always using the same mapping blocks
* it is not necessary to explicitly add a new frame set - it will
* be added automatically when adding data for a frame */
@@ -383,7 +383,7 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj)
}
frame_nr = i * n_frames_per_frame_set;
-
+
for(k=0; k<300; k++)
{
mapping[k]=k;
@@ -470,7 +470,7 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj)
}
}
}
-
+
free(molpos);
free(data);
@@ -481,7 +481,7 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj)
#endif
stat = tng_file_headers_read(traj, TNG_SKIP_HASH);
-
+
while(stat == TNG_SUCCESS)
{
stat = tng_frame_set_read_next(traj, TNG_SKIP_HASH);
@@ -582,7 +582,7 @@ int main()
tng_trajectory_t traj;
tng_function_status stat;
char time_str[TNG_MAX_DATE_STR_LEN];
-
+
if(tng_trajectory_init(&traj) != TNG_SUCCESS)
{
tng_trajectory_destroy(&traj);
@@ -614,7 +614,7 @@ int main()
{
printf("Test Read and write file:\t\t\tSucceeded.\n");
}
-
+
if(tng_test_get_box_data(traj) != TNG_SUCCESS)
{
printf("Test Get data:\t\t\t\t\tFailed. %s: %d\n",
@@ -635,7 +635,7 @@ int main()
{
printf("Test Destroy and init trajectory:\t\tSucceeded.\n");
}
-
+
#ifdef EXAMPLE_FILES_DIR
tng_output_file_set(traj, EXAMPLE_FILES_DIR "tng_test.tng");
@@ -652,7 +652,7 @@ int main()
{
printf("Test Write and read file:\t\t\tSucceeded.\n");
}
-
+
if(tng_test_get_positions_data(traj) != TNG_SUCCESS)
{
printf("Test Get particle data:\t\t\t\tFailed. %s: %d\n",
@@ -674,7 +674,7 @@ int main()
printf("Test Destroy trajectory:\t\t\tSucceeded.\n");
}
-
+
#ifdef EXAMPLE_FILES_DIR
stat = tng_util_trajectory_open(EXAMPLE_FILES_DIR "tng_test.tng", 'r', &traj);
#else
@@ -691,7 +691,7 @@ int main()
printf("Test Utility function open:\t\t\tSucceeded.\n");
}
- stat = tng_util_trajectory_close(&traj);
+ stat = tng_util_trajectory_close(&traj);
if(stat != TNG_SUCCESS)
{
printf("Test Utility function close:\t\t\tFailed. %s: %d.\n",
@@ -702,8 +702,8 @@ int main()
{
printf("Test Utility function close:\t\t\tSucceeded.\n");
}
-
+
printf("Tests finished\n");
-
+
exit(0);
} \ No newline at end of file
diff --git a/src/tests/tng_parallel_read.c b/src/tests/tng_parallel_read.c
index d0aaa15..824fc73 100644
--- a/src/tests/tng_parallel_read.c
+++ b/src/tests/tng_parallel_read.c
@@ -21,7 +21,7 @@
/* N.B. this code is for testing parallel reading of trajectory frame sets. The
* performance is not improved very much and is to a large extent limited by
* disk i/o. It can however be used as inspiration for writing parallel code
- * using the TNG library. */
+ * using the TNG library. The code is NOT fully tested and may behave strangely. */
int main(int argc, char **argv)
{
@@ -29,9 +29,9 @@ int main(int argc, char **argv)
union data_values ***local_positions = 0; // A 3-dimensional array to be populated
union data_values **particle_pos = 0;
int64_t n_particles, n_values_per_frame, n_frame_sets, n_frames;
- int64_t n_frames_per_frame_set;
+ int64_t n_frames_per_frame_set, tot_n_frames = 0;
char data_type;
- int i, j;
+ int i, j, fail;
int64_t particle = 0, local_first_frame, local_last_frame;
char atom_name[64], res_name[64];
tng_trajectory_frame_set_t frame_set = 0;
@@ -66,7 +66,7 @@ int main(int argc, char **argv)
tng_num_frame_sets_get(traj, &n_frame_sets);
tng_num_frames_per_frame_set_get(traj, &n_frames_per_frame_set);
- particle_pos = malloc(sizeof(union data_values **) * n_frame_sets *
+ particle_pos = malloc(sizeof(union data_values *) * n_frame_sets *
n_frames_per_frame_set);
for(i = n_frame_sets * n_frames_per_frame_set; i--;)
{
@@ -89,12 +89,14 @@ int main(int argc, char **argv)
{
printf("Particle name not found\n");
}
+
+ fail = 0;
#pragma omp parallel \
private (n_frames, n_particles, n_values_per_frame, \
- local_first_frame, local_last_frame, j) \
+ local_first_frame, local_last_frame, j, fail) \
firstprivate (local_traj, local_positions, frame_set)\
-shared(data_type, traj, n_frame_sets, particle_pos, particle, i)\
+shared(data_type, traj, n_frame_sets, particle_pos, particle, i, tot_n_frames)\
default(none)
{
/* Each tng_trajectory_t keeps its own file pointers and i/o positions.
@@ -106,22 +108,30 @@ default(none)
if(tng_frame_set_nr_find(local_traj, i) != TNG_SUCCESS)
{
printf("FAILED finding frame set %d!\n", i);
+ tot_n_frames = 0;
+ fail = 1;
}
if(tng_particle_data_get(local_traj, TNG_TRAJ_POSITIONS, &local_positions,
&n_frames, &n_particles, &n_values_per_frame,
&data_type) != TNG_SUCCESS)
{
printf("FAILED getting particle data\n");
+ tot_n_frames = 0;
+ fail = 1;
}
- tng_current_frame_set_get(local_traj, &frame_set);
- tng_frame_set_frame_range_get(local_traj, frame_set, &local_first_frame, &local_last_frame);
-// printf("Frame %"PRId64"-%"PRId64":\n", local_first_frame, local_last_frame);
-// printf("%"PRId64" %"PRId64" %"PRId64"\n", n_frames, n_particles, n_values_per_frame);
- for(j = 0; j < n_frames; j++)
+ if(!fail)
{
- particle_pos[local_first_frame + j][0] = local_positions[j][particle][0];
- particle_pos[local_first_frame + j][1] = local_positions[j][particle][1];
- particle_pos[local_first_frame + j][2] = local_positions[j][particle][2];
+ tng_current_frame_set_get(local_traj, &frame_set);
+ tng_frame_set_frame_range_get(local_traj, frame_set, &local_first_frame, &local_last_frame);
+ // printf("Frame %"PRId64"-%"PRId64":\n", local_first_frame, local_last_frame);
+ // printf("%"PRId64" %"PRId64" %"PRId64"\n", n_frames, n_particles, n_values_per_frame);
+ tot_n_frames += n_frames;
+ for(j = 0; j < n_frames; j++)
+ {
+ particle_pos[local_first_frame + j][0] = local_positions[j][particle][0];
+ particle_pos[local_first_frame + j][1] = local_positions[j][particle][1];
+ particle_pos[local_first_frame + j][2] = local_positions[j][particle][2];
+ }
}
}
@@ -136,24 +146,24 @@ default(none)
switch(data_type)
{
case TNG_INT_DATA:
- for(i = 0; i < n_frame_sets * n_frames_per_frame_set; i++)
+ for(j = 0; j < tot_n_frames; j++)
{
- printf("\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", particle_pos[i][0].i,
- particle_pos[i][1].i, particle_pos[i][2].i);
+ printf("\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", particle_pos[j][0].i,
+ particle_pos[j][1].i, particle_pos[j][2].i);
}
break;
case TNG_FLOAT_DATA:
- for(i = 0; i < n_frame_sets * n_frames_per_frame_set; i++)
+ for(j = 0; j < tot_n_frames; j++)
{
- printf("\t%f\t%f\t%f\n", particle_pos[i][0].f,
- particle_pos[i][1].f, particle_pos[i][2].f);
+ printf("\t%f\t%f\t%f\n", particle_pos[j][0].f,
+ particle_pos[j][1].f, particle_pos[j][2].f);
}
break;
case TNG_DOUBLE_DATA:
- for(i = 0; i < n_frame_sets * n_frames_per_frame_set; i++)
+ for(j = 0; j < tot_n_frames; j++)
{
- printf("\t%f\t%f\t%f\n", particle_pos[i][0].d,
- particle_pos[i][1].d, particle_pos[i][2].d);
+ printf("\t%f\t%f\t%f\n", particle_pos[j][0].d,
+ particle_pos[j][1].d, particle_pos[j][2].d);
}
break;
default:
contact: Jan Huwald // Impressum