[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
[netCDF #GDV-269599]: remove strlen calls in inner loops of NC_finddim and NC_findvar -- hash version

Subject: [netCDF #GDV-269599]: remove strlen calls in inner loops of NC_finddim and NC_findvar -- hash version
Date: Thu, 12 Aug 2010 13:56:00 -0600
Hi Greg,

> Thanks.  If you have a different hash code that doesn't cause licensing
> issues, feel free to replace what I used if it makes you life easier.

I did that, and it's in the latest snapshot.  I used the Jenkins lookup3.c
code and also defined VALGRIND to have it not try to read to the nearest
containing multiple of 4 bytes.  

When it's convenient, we'd be interested to know if the resulting speedup
is as expected and if it's close enough to the Paul Hsieh code that you can
use it.

--Russ

> On 07/15/2010 01:49 PM, Unidata netCDF Support wrote:
> > Hi Greg,
> >
> >
> >> I had forgotten about this, but noticed that it doesn't show up in the
> >> latest 4.1.2-beta1.  I am still very interested in having this
> >> included.  We have been using it internally at Sandia for the past 7
> >> months and it gives us a significant speedup on large models and we
> >> haven't seen any issues with it on normal-sized models.
> >>
> > Thanks for the reminder.  It looks like Ed and I each had assumed the other
> > would include this, so it fell through.  I'll commit to getting it in the
> > 4.1.2 release and let you know when it's available in a snapshot of beta
> > before then.
> >
> > I'm currently puzzling over the licensing terms, trying to decide between
> > the "Paul Hsieh OLD BSD license", which would require an addition of the
> > license to our documentation, versus the "Paul Hsieh exposition license",
> > which would require that I get prior consent, because it's an excerpt from
> > his web site.  I think I'll try the latter while I'm working on including
> > the code.
> >
> > --Russ
> >
> >
> >> if you would like a new patch against current source, let me know and i
> >> will regenerate.
> >>
> >> --Greg
> >>
> >> On 12/08/2009 08:44 AM, Greg Sjaardema wrote:
> >>
> >>> Thanks, I definitely agree with your decision.  Delaying the patch
> >>> will give time to examine its pros and cons in more detail.
> >>> --Greg
> >>>
> >>> Unidata netCDF Support wrote:
> >>>
> >>>> Hi Greg,
> >>>>
> >>>> Thanks for all your work on this enhancement and for providing
> >>>> the patch.
> >>>>
> >>>> We have reluctantly decided that it's too late and a little to
> >>>> risky for us to include this optimization in version 4.1, but
> >>>> will include it in the snapshots and releases after that.
> >>>>
> >>>> --Russ
> >>>>
> >>>>
> >>>>
> >>>>> Attached is another patch that passes the netcdf regression tests, but
> >>>>> is an improvement over my previous 'lenstr' patch (#TZM-335067).
> >>>>> Basically, I added a 'hash' field to both NC_var and NC_dim which
> >>>>> maintains a hash of the string  'name->cp' field.  There is then code in
> >>>>> dim.c and var.c to update the hash field during var and dim creation and
> >>>>> renaming.  The hash value is used in the NC_finddim and NC_findvar inner
> >>>>> loops instead of doing "strlen((*loc)->name->cp)".  For the file I that
> >>>>> motivated this, I reduced the strlen calls from 476,952,472 to 389,810
> >>>>> (43.6% of execution time down to 0.25%) and also reduced the strncmp
> >>>>> calls.   To account for possible hash collisions, it still does the
> >>>>> strncmp call if the hashes match.
> >>>>>
> >>>>> I put the hash code in var.c which probably isn't the correct location,
> >>>>> but it avoided me having to add new files...  The hash code I used was
> >>>>> SuperFastHash from http://www.azillionmonkeys.com/qed/hash.html.
> >>>>>
> >>>>> I realize that this patch may not be of general usage and only provides
> >>>>> a measurable speedup for very large files, but it is also not very
> >>>>> intrusive.  It does increase NC_dim size by a non-negligible amount (3
> >>>>> size_t + string vs 2 size_t + string).
> >>>>>
> >>>>> Anyway, here it is if you want it.  Let me know if you want it cleaned
> >>>>> up or any renamings.
> >>>>> --Greg
> >>>>>
> >>>>> diff -crB netcdf-4.1-beta2/libsrc/dim.c 
> >>>>> netcdf-4.1-beta2-new/libsrc/dim.c
> >>>>> *** netcdf-4.1-beta2/libsrc/dim.c 2009-02-20 13:34:55.000000000 -0700
> >>>>> --- netcdf-4.1-beta2-new/libsrc/dim.c     2009-12-04 10:54:20.000000000 
> >>>>> -0700
> >>>>> ***************
> >>>>> *** 38,43 ****
> >>>>> --- 38,44 ----
> >>>>> return NULL;
> >>>>>
> >>>>> dimp->name = name;
> >>>>> +         dimp->hash = SuperFastHash(name->cp, strlen(name->cp));
> >>>>> dimp->size = 0;
> >>>>>
> >>>>> return(dimp);
> >>>>> ***************
> >>>>> *** 127,133 ****
> >>>>> {
> >>>>>
> >>>>> int dimid;
> >>>>> !    size_t slen;
> >>>>> NC_dim ** loc;
> >>>>> char *name;
> >>>>>
> >>>>> --- 128,134 ----
> >>>>> {
> >>>>>
> >>>>> int dimid;
> >>>>> !    uint32_t shash;
> >>>>> NC_dim ** loc;
> >>>>> char *name;
> >>>>>
> >>>>> ***************
> >>>>> *** 143,153 ****
> >>>>> name = (char *)utf8proc_NFC((const unsigned char *)uname);
> >>>>> if(name == NULL)
> >>>>> return NC_ENOMEM;
> >>>>> !       slen = strlen(name);
> >>>>>
> >>>>> for(; (size_t) dimid < ncap->nelems
> >>>>> !              && (strlen((*loc)->name->cp) != slen
> >>>>> !                  || strncmp((*loc)->name->cp, name, slen) != 0);
> >>>>> dimid++, loc++)
> >>>>> {
> >>>>> /*EMPTY*/
> >>>>> --- 144,154 ----
> >>>>> name = (char *)utf8proc_NFC((const unsigned char *)uname);
> >>>>> if(name == NULL)
> >>>>> return NC_ENOMEM;
> >>>>> !       shash = SuperFastHash(name, strlen(name));
> >>>>>
> >>>>> for(; (size_t) dimid < ncap->nelems
> >>>>> !              && ((*loc)->hash != shash
> >>>>> !                  || strncmp((*loc)->name->cp, name, strlen(name)) != 
> >>>>> 0);
> >>>>> dimid++, loc++)
> >>>>> {
> >>>>> /*EMPTY*/
> >>>>> ***************
> >>>>> *** 524,529 ****
> >>>>> --- 525,531 ----
> >>>>> if(newStr == NULL)
> >>>>> return NC_ENOMEM;
> >>>>> dimp->name = newStr;
> >>>>> +                 dimp->hash = SuperFastHash(newStr->cp, 
> >>>>> strlen(newStr->cp));
> >>>>> free_NC_string(old);
> >>>>> return NC_NOERR;
> >>>>> }
> >>>>> ***************
> >>>>> *** 531,536 ****
> >>>>> --- 533,539 ----
> >>>>> /* else, not in define mode */
> >>>>>
> >>>>> status = set_NC_string(dimp->name, newname);
> >>>>> +         dimp->hash = SuperFastHash(newname, strlen(newname));
> >>>>> free(newname);
> >>>>> if(status != NC_NOERR)
> >>>>> return status;
> >>>>> diff -crB netcdf-4.1-beta2/libsrc/nc.h netcdf-4.1-beta2-new/libsrc/nc.h
> >>>>> *** netcdf-4.1-beta2/libsrc/nc.h  2009-02-24 14:12:40.000000000 -0700
> >>>>> --- netcdf-4.1-beta2-new/libsrc/nc.h      2009-12-04 10:55:05.000000000 
> >>>>> -0700
> >>>>> ***************
> >>>>> *** 12,17 ****
> >>>>> --- 12,18 ----
> >>>>> #include <config.h>
> >>>>>
> >>>>> #include  <stddef.h>      /* size_t */
> >>>>> + #include        <stdint.h>      /* uint32_t */
> >>>>> #include  <sys/types.h>   /* off_t */
> >>>>> #include  "netcdf.h"
> >>>>> #include  "ncio.h"        /* ncio */
> >>>>> ***************
> >>>>> *** 77,82 ****
> >>>>> --- 78,84 ----
> >>>>> typedef struct {
> >>>>> /* all xdr'd */
> >>>>> NC_string *name;
> >>>>> +         uint32_t hash;
> >>>>> size_t size;
> >>>>> } NC_dim;
> >>>>>
> >>>>> ***************
> >>>>> *** 175,180 ****
> >>>>> --- 177,183 ----
> >>>>> size_t *dsizes; /* compiled info: the right to left product of shape */
> >>>>> /* below gets xdr'd */
> >>>>> NC_string *name;
> >>>>> +         uint32_t hash;
> >>>>> /* next two: formerly NC_iarray *assoc */ /* user definition */
> >>>>> size_t ndims;     /* assoc->count */
> >>>>> int *dimids;      /* assoc->value */
> >>>>> ***************
> >>>>> *** 194,199 ****
> >>>>> --- 197,205 ----
> >>>>>
> >>>>> /* Begin defined in var.c */
> >>>>>
> >>>>> + extern uint32_t
> >>>>> + SuperFastHash (const char * data, int len);
> >>>>> +
> >>>>> extern void
> >>>>> free_NC_var(NC_var *varp);
> >>>>>
> >>>>> diff -crB netcdf-4.1-beta2/libsrc/var.c 
> >>>>> netcdf-4.1-beta2-new/libsrc/var.c
> >>>>> *** netcdf-4.1-beta2/libsrc/var.c 2009-02-20 13:35:07.000000000 -0700
> >>>>> --- netcdf-4.1-beta2-new/libsrc/var.c     2009-12-04 10:54:01.000000000 
> >>>>> -0700
> >>>>> ***************
> >>>>> *** 52,57 ****
> >>>>> --- 52,58 ----
> >>>>>
> >>>>> varp->name = strp;
> >>>>> varp->ndims = ndims;
> >>>>> +         varp->hash = SuperFastHash(strp->cp, strlen(strp->cp));
> >>>>>
> >>>>> if(ndims != 0)
> >>>>> {
> >>>>> ***************
> >>>>> *** 302,308 ****
> >>>>> NC_findvar(const NC_vararray *ncap, const char *uname, NC_var **varpp)
> >>>>> {
> >>>>> NC_var **loc;
> >>>>> !         size_t slen;
> >>>>> int varid;
> >>>>> char *name;
> >>>>>
> >>>>> --- 303,309 ----
> >>>>> NC_findvar(const NC_vararray *ncap, const char *uname, NC_var **varpp)
> >>>>> {
> >>>>> NC_var **loc;
> >>>>> !         uint32_t shash;
> >>>>> int varid;
> >>>>> char *name;
> >>>>>
> >>>>> ***************
> >>>>> *** 317,328 ****
> >>>>> name = (char *)utf8proc_NFC((const unsigned char *)uname);
> >>>>> if(name == NULL)
> >>>>> return NC_ENOMEM;
> >>>>> !         slen = strlen(name);
> >>>>>
> >>>>> for(varid = 0; (size_t) varid < ncap->nelems; varid++, loc++)
> >>>>> {
> >>>>> !                 if(strlen((*loc)->name->cp) == slen &&
> >>>>> !                         strncmp((*loc)->name->cp, name, slen) == 0)
> >>>>> {
> >>>>> if(varpp != NULL)
> >>>>> *varpp = *loc;
> >>>>> --- 318,329 ----
> >>>>> name = (char *)utf8proc_NFC((const unsigned char *)uname);
> >>>>> if(name == NULL)
> >>>>> return NC_ENOMEM;
> >>>>> !         shash = SuperFastHash(name, strlen(name));
> >>>>>
> >>>>> for(varid = 0; (size_t) varid < ncap->nelems; varid++, loc++)
> >>>>> {
> >>>>> !                 if((*loc)->hash == shash &&
> >>>>> !                    strncmp((*loc)->name->cp, name, strlen(name)) == 0)
> >>>>> {
> >>>>> if(varpp != NULL)
> >>>>> *varpp = *loc;
> >>>>> ***************
> >>>>> *** 817,828 ****
> >>>>> --- 818,831 ----
> >>>>> if(newStr == NULL)
> >>>>> return(-1);
> >>>>> varp->name = newStr;
> >>>>> +                 varp->hash = SuperFastHash(newStr->cp, 
> >>>>> strlen(newStr->cp));
> >>>>> free_NC_string(old);
> >>>>> return NC_NOERR;
> >>>>> }
> >>>>>
> >>>>> /* else, not in define mode */
> >>>>> status = set_NC_string(varp->name, newname);
> >>>>> +         varp->hash = SuperFastHash(newname, strlen(newname));
> >>>>> free(newname);
> >>>>> if(status != NC_NOERR)
> >>>>> return status;
> >>>>> ***************
> >>>>> *** 838,840 ****
> >>>>> --- 841,900 ----
> >>>>>
> >>>>> return NC_NOERR;
> >>>>> }
> >>>>> +
> >>>>> + #include <stdint.h>
> >>>>> + #undef get16bits
> >>>>> + #if (defined(__GNUC__) && defined(__i386__)) || defined(__WATCOMC__) \
> >>>>> +   || defined(_MSC_VER) || defined (__BORLANDC__) || defined 
> >>>>> (__TURBOC__)
> >>>>> + #define get16bits(d) (*((const uint16_t *) (d)))
> >>>>> + #endif
> >>>>> +
> >>>>> + #if !defined (get16bits)
> >>>>> + #define get16bits(d) ((((uint32_t)(((const uint8_t *)(d))[1])) << 8)\
> >>>>> +                        +(uint32_t)(((const uint8_t *)(d))[0]) )
> >>>>> + #endif
> >>>>> +
> >>>>> + uint32_t SuperFastHash (const char * data, int len) {
> >>>>> + uint32_t hash = len, tmp;
> >>>>> + int rem;
> >>>>> +
> >>>>> +     if (len <= 0 || data == 0) return 0;
> >>>>> +
> >>>>> +     rem = len & 3;
> >>>>> +     len >>= 2;
> >>>>> +
> >>>>> +     /* Main loop */
> >>>>> +     for (;len > 0; len--) {
> >>>>> +         hash  += get16bits (data);
> >>>>> +         tmp    = (get16bits (data+2) << 11) ^ hash;
> >>>>> +         hash   = (hash << 16) ^ tmp;
> >>>>> +         data  += 2*sizeof (uint16_t);
> >>>>> +         hash  += hash >> 11;
> >>>>> +     }
> >>>>> +
> >>>>> +     /* Handle end cases */
> >>>>> +     switch (rem) {
> >>>>> +         case 3: hash += get16bits (data);
> >>>>> +                 hash ^= hash << 16;
> >>>>> +                 hash ^= data[sizeof (uint16_t)] << 18;
> >>>>> +                 hash += hash >> 11;
> >>>>> +                 break;
> >>>>> +         case 2: hash += get16bits (data);
> >>>>> +                 hash ^= hash << 11;
> >>>>> +                 hash += hash >> 17;
> >>>>> +                 break;
> >>>>> +         case 1: hash += *data;
> >>>>> +                 hash ^= hash << 10;
> >>>>> +                 hash += hash >> 1;
> >>>>> +     }
> >>>>> +
> >>>>> +     /* Force "avalanching" of final 127 bits */
> >>>>> +     hash ^= hash << 3;
> >>>>> +     hash += hash >> 5;
> >>>>> +     hash ^= hash << 4;
> >>>>> +     hash += hash >> 17;
> >>>>> +     hash ^= hash << 25;
> >>>>> +     hash += hash >> 6;
> >>>>> +
> >>>>> +     return hash;
> >>>>> + }
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>> Russ Rew                                         UCAR Unidata Program
> >>>> address@hidden                     http://www.unidata.ucar.edu
> >>>>
> >>>>
> >>>>
> >>>> Ticket Details
> >>>> ===================
> >>>> Ticket ID: GDV-269599
> >>>> Department: Support netCDF
> >>>> Priority: Normal
> >>>> Status: Closed
> >>>>
> >>>>
> >>>>
> >>>>
> >>
> >>
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: GDV-269599
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> >
> 
> 

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: GDV-269599
Department: Support netCDF
Priority: Critical
Status: Closed
Prev by Date: [netCDF #YZY-706323]: problem with nf90_open (fortran90)
Next by Date: [netCDF #IHH-601955]: [netcdfgroup] Allowed characters in variable names?
Previous by thread: [netCDF #GDV-269599]: remove strlen calls in inner loops of NC_finddim and NC_findvar -- hash version
Next by thread: [netCDF #TFD-790939]: netCDF4 support - multiple fill values
Index(es):
- Date
- Thread