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Re: [infomap-nlp-users] RE: Infomap & 64-bit
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From: <lei...@gm...> - 2005-05-20 07:13:06
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Hi,
maybe you have solved this already, but one thing I had to do was to fix=
=20
this function in myutils.c:
float **Allocate_Float_Matrix( int N, int M )
{
float *workp, **p;
int i, j;
if ((p =3D (float **) malloc((unsigned) N * (M + 1) *
sizeof(float))) =3D=3D NULL)
errormessage("allocate_float","",NON);
workp =3D ((float *) p) + N;
for (i =3D j =3D 0; i < N; i++, j +=3D M)
p[i] =3D &workp[j];
return p;
}
The array contains bot floats and float pointers, which will work in 32bit=
=20
even if it's ugly code...
This version works both in 64 and 32bit:
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float **Allocate_Float_Matrix( int N, int M ) {
float *workp, **p;
int i, j;
if(!(p =3D malloc(N * sizeof(float *))))=20
errormessage("allocate_float","",NON);
for(i=3D0; i<N; i++) {
if(!(p[i] =3D malloc(M*sizeof(float)))) errormessage("allocate_float","",NO=
N);=20
}
return p;
}
Regards,
Leif
On 5/19/05, Deane, Paul <pd...@et...> wrote:=20
>=20
> Yes, cc'ing this discussion to the infomap list would be excellent.=20
> Daniel,
> could you give them the breakdown on the crashes we've been experiencing?
>=20
>=20
> -----Original Message-----
> From: Scott Cederberg [mailto:ced...@gm...]
> Sent: Thursday, May 19, 2005 4:59 PM
> To: Deane, Paul
> Cc: Dominic Widdows; bea...@im...; Zuckerman, Daniel;
> inf...@li...
> Subject: Re: Infomap & 64-bit
>=20
> Hi Paul,
>=20
> I'd be happy to be put in touch with Daniel to see if we can
> replicate the problem for debugging. If you're comfortable carrying
> on this discussion on the infomap-nlp-users list, let's do that so it can
> be useful for other people. (I'd been ignoring the lists for a while but=
=20
> am
> now reading them again.)
>=20
> It's going to take me a little while to refresh my memory as to how
> all this stuff works, but I'd like to root out the problem so the softwar=
e
> can scale to 64-bit systems in the future.
>=20
>=20
> Scott
>=20
> On 5/18/05, Deane, Paul <pd...@et...> wrote:
> > Here's my original post to the infomap list on this issue. We're
> > running Gentoo linux, and one problem we encountered when trying to
> > get it to compile was that the paths for ndbm.h didn't match the setup
> > on our machine, so we had to create a symbolic link -- so that's a
> > possible compatibility issue. However, the crash we get on the 64 bit
> > machine's down in svdinterface.
> >
> > I'm cc'ing the programmer who's been working on this, Daniel
> > Zuckerman, to keep him in the loop. Thanks if you're able to help
> > here. Ideal would be if Daniel could send you the details of the
> > scaleup problems we've had and see if you could replicate them -- we
> > had a problem on 32-bit when we tried to increase the size of the=20
> default
> SVD analysis, also.
> >
> > ----------------------------------------------------------------------
> > ----
> >
> > Has anyone successfully compiled infomap on 64-bit linux? (AMD 64
> > running Debian with 64-bit libraries only).
> >
> > When I tried to compile 0.8.5 (using the 64-bit version of GCC), I get
> > the following error messages during compile:
> >
> > myutils.c: In function `mymalloc':
> > myutils.c:167: error: conflicting types for 'malloc'
> > make[3]: *** [myutils.o] Error 1
> > make[2]: *** [all-recursive] Error 1
> > make[1]: *** [all-recursive] Error 1
> >
> > When I comment out the offending line, it compiles, but I get memory
> > errors when I attempt to run the program, i.e., the end of the log look=
s
> like this:
> >
> > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D
> > Building target: /export/home/bragi2/pdeane/test/left
> > Prerequisites: /export/home/bragi2/pdeane/test/coll
> > /export/home/bragi2/pdeane/t
> > est/indx
> > Fri Apr 29 09:06:56 EDT 2005
> > ..................................................
> > cd /export/home/bragi2/pdeane/test && rm svd_diag left \
> > rght sing
> > rm: cannot remove `svd_diag': No such file or directory
> > rm: cannot remove `left': No such file or directory
> > rm: cannot remove `rght': No such file or directory
> > rm: cannot remove `sing': No such file or directory
> > make: [/export/home/bragi2/pdeane/test/left] Error 1 (ignored) cd
> > /export/home/bragi2/pdeane/test && svdinterface \
> > -singvals 100 \
> > -iter 100
> >
> > This is svdinterface.
> >
> > Writing to: left
> > Writing to: rght
> > Writing to: sing
> > Writing to: svd_diag
> > Reading: indx
> > Reading: indx
> > Reading: coll
> > make: *** [/export/home/bragi2/pdeane/test/left] Error 139
> > ----------------------------------------------------------------------
> > ------
> > -----------------
> >
> > When I check the directory the model was being created in, this is the
> > state of things, with the evidence suggesting that something when
> > nastily wrong in the svdinterface code that calls the mymalloc
> > function:
> >
> > -rw-r--r-- 1 pdeane nlp 2819650 Apr 29 09:06 coll
> > -rw-r--r-- 1 pdeane nlp 374 Apr 29 09:06 corpus_format.bin
> > -rw-r--r-- 1 pdeane nlp 157223 Apr 29 09:06 dic
> > -rw-r--r-- 1 pdeane nlp 3939 Apr 29 09:06 indx
> > -rw-r--r-- 1 pdeane nlp 0 Apr 29 09:06 left
> > -rw-r--r-- 1 pdeane nlp 28 Apr 29 09:06 model_info.bin
> > -rw-r--r-- 1 pdeane nlp 16396 Apr 29 09:06 model_params.bin
> > -rw-r--r-- 1 pdeane nlp 4 Apr 29 09:06 numDocs
> > -rw-r--r-- 1 pdeane nlp 0 Apr 29 09:06 rght
> > -rw-r--r-- 1 pdeane nlp 0 Apr 29 09:06 sing
> > -rw-r--r-- 1 pdeane nlp 0 Apr 29 09:06 svd_diag
> > -rw-r--r-- 1 pdeane nlp 540345 Apr 29 09:06 wordlist
> >
> > I tried changing the defines e.g. BIGINT, BIGFLOAT in fixed.h to
> > 64-bit values but this makes no difference, and that was the only
> > obvious 32-bit dependency I could see.
> >
> > Interestingly, the original SVDPACKC compiles and runs in my
> > environment, so whatever is going on looks like it must be a function
> > of the svdinterface code and associated changes. Also, btw, I have had
> > no problem running infomap on a 32-bit linux machine nor under cygwin o=
n=20
> a
> windows machine.
> >
> > Can anybody help me out here?
> >
> >
> >
> >
> > -----Original Message-----
> > From: Dominic Widdows [mailto:dwi...@cs...]
> > Sent: Wednesday, May 18, 2005 10:01 AM
> > To: Deane, Paul
> > Cc: ced...@gm...; bea...@im...
> > Subject: Re: Infomap & 64-bit
> >
> > Hi Scott,
> >
> > Sorry to bother you during your vacation, but do you have any idea why
> > the infomap software may fail to run on a 64-bit machine?
> >
> > BTW, Paul, I believe there is a "matlab file" output option in the
> > infomap code, which outputs the raw counts to a matlab-compatible
> > sparse matrix format. This would probably make it easy for you to
> > separate the problem into counting coocurrences and then performing the
> SVD in a separate stage.
> > I'm cc'ing Beate Dorow, since she worked on this a few years ago.
> >
> > Best wishes,
> > Dominic
> >
> > On Wed, 18 May 2005, Deane, Paul wrote:
> >
> > > Hi, seeing your post today on the infomap mailing list prompts me to
> > > repeat a query.
> > >
> > > I've been trying to get infomap working on a large 64-bit machine
> > > running Linux, and my post to this list outlined my problems. Reason
> > > I'm doing this is I want to run analyses on some very large corpora,
> > > and infomap doesn't seem to scale up well to these very large
> > > corpora when I run them on our 32-bit machines ... something always
> > > breaks and we get memory errors when we increase the number of words
> > > we want to cover and/or the size of the corpus up toward our target,
> > > which is 100,000 words of vocabulary on a 500-million-word corpus.
> > >
> > > Is there a chance of getting any help here? If we can't get past the
> > > scaleup problems, we'll have to do the analysis outside of infomap,
> > > i.e., compile the counts and do the SVD indepedently.
> > >
> > > Thanks,
> > >
> > > Paul Deane
> > >
> > >
> > >
> > > ********************************************************************
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> *************************************************************************=
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l
> in error, please notify the sender; do not disclose, copy, distribute, or
> take any action in reliance on the contents of this information; and=20
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>=20
--=20
Leif Gr=F6nqvist, GSLT, le...@li...,
www.ling.gu.se/~leifg<http://www.ling.gu.se/~leifg>,
031-821515(home)
School of Mathematics and Systems Engineering, V=E4xj=F6 University=20
0707164380(mob)
Department of Linguistics, G=F6teborg University, +46 31 773 1177, 773=20
4853(fax)
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