library problem again!!!

Printable View

07-12-2006
kris.c

library problem again!!!

I have to link plenty of libraries here and its getting all messy:

Here's a list of libraries that i have to link :
1. fftw-3.1.1 at /compiler/fftw3.1.1
2. fftw-2.1.5 at /compiler/fftw-2.1.5
3. acml3.1.0 at /compiler/acml3.1.0

acml3.1.0 uses pathcc and pathfortran , so that are to be linked
to enable the threading I have to include libfftw_threads.a and libpthread.a too

Code:

mpicc fourier_pc.o -I/compiler/fftw-3.1.1/include -I/compiler/fftw-2.1.5/include -L/usr/lib -L/compiler/fftw-3.1.1/lib -L/compiler/fftw-2.1.5/lib -L/compiler/acml3.1.0/pathscale64/lib -L/compiler/pathscale/lib/2.4 -lfftw3 -lacml -lacml_mv -lpathfortran -lfftw_threads -lpthread -lm /usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread /usr/bin/ld: skipping incompatible /usr/lib/libpthread.a when searching for -lpthread /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread /usr/bin/ld: skipping incompatible /usr/lib/libpthread.a when searching for -lpthread /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc fourier_pc.o(.text+0x3b): In function `main': : undefined reference to `fftw_init_threads' fourier_pc.o(.text+0x11b): In function `main': : undefined reference to `fftw_plan_with_nthreads' fourier_pc.o(.text+0x1f1): In function `main': : undefined reference to `fftw_cleanup_threads' collect2: ld returned 1 exit status

not able to make out what

[code]

/usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread

[/code

really means..

pretty sure, those undefined references will go once the "libthread.a" is linked properly
07-12-2006
itsme86

Are you using a 64-bit library on a 32-bit OS or vice versa?
07-12-2006
kris.c

I have no idea.. I am working on a cluster..
How do i find out?
07-12-2006
kris.c

slightly better ..still not good enough

Some development :

Code:

my prog name is fourier_pc.c 1. the location of fftw-3.1.1 is : /compiler/fftw-3.1.1 the contents of the lib dir are : libfftw3.a libfftw3.la pkgconfig the contents of the include dir are : fftw3.f fftw3.h 2.the location of the threaded version of fftw-3.1.1 is : /compiler/fftw-3.1.1-dp-threads the contents of the lib dir are : libfftw3l.a libfftw3l.la libfftw3l_threads.a libfftw3l_threads.la pkgconfig the contents of the include dir are : fftw3.f fftw3.h 3. the location of ACML is : /compiler THis is what i have done till noiw : $> pathcc -c -I/compiler/fftw-3.1.1/include fourier_pc.c -L/compiler/fftw-3.1.1/lib -lfftw3 $> gcc fourier_pc.o -L/compiler/fftw-3.1.1/lib -L/compiler/fftw-3.1.1-dp-threads/lib -L/compiler/acml3.1.0/pathscale64/lib -L/compiler/pathscale/lib/2.4 -lpthread -lfftw3l_threads -lfftw3 -lacml -lacml_mv -lpathfortran -lm and these are the error message si am getting : fourier_pc.o(.text+0x38): In function `main': : undefined reference to `fftw_init_threads' fourier_pc.o(.text+0xb2): In function `main': : undefined reference to `fftw_plan_with_nthreads' fourier_pc.o(.text+0x189): In function `main': : undefined reference to `fftw_cleanup_threads' collect2: ld returned 1 exit status

I have tried all kinds of combinations with -lpthread -lfftw3l_threads -lfftw3 ...I still get the same set of messages..
I need help badly, with this
07-13-2006
Salem

> : undefined reference to `fftw_init_threads'
Are you sure you spelled these correctly?

You can see what symbols a library exports by doing something like
nm /compiler/fftw-3.1.1-dp-threads/lib/libfftw3l_threads.a

Do the symbols you're looking for exist in that library?

Are there no readme / howto / FAQ entries describing the command line for what you're trying?
07-13-2006
kris.c

> Are you sure you spelled these correctly?
I am copy pasting the messages..

well, anyway .. today mor my project guide told me more about the version fftw-2.1.5 that supports mpi . Looking at that now, its a neat package that combines the best of both fftw and mpi..
I think i can take it from here...

OK, I need one HUGE doubt here..
What is the difference between implementing FFTW transform using multi threading and using MPI?
Is multi threading allowed for systems with distributed memory or is it only for shared memory devices?
If it is allowed for distributed systems how can the threads communicate between each other..

The mistake i was commiting (like an idiot) was splitting up the input array into " p " partitions if i am working with " p " processors. And issusing one partition to one processor. Naturally this gave me the wrong result . An 1000 -point fourier transform is different from a 250 point transform ( if the original size is 1000 and i am using 4 processors.. If I have to follow the same method of partitioning , any ideas how to do it with multi-threading?

thanks
07-13-2006
Salem

> > Are you sure you spelled these correctly?
> I am copy pasting the messages..
It's not that I'm worried about.
Writing fftw_init_threads in the code and the library defines fftwInitThreads is one reason why the error message might appear.

MPI and/or threading is only going to do you any good if you have more than one physical processor to hand. Otherwise you're just wasting time copying stuff around and switching contexts (all on the same processor).

In addition, the cost of MPI has to be small compared to the work to be performed. There's little point in spending a second transferring the work if it only takes half a second to do the work.
07-13-2006
kris.c

>MPI and/or threading is only going to do you any good if you have more than one physical processor to hand.
I have mentioned earlier , I am working on a cluster..

>In addition, the cost of MPI has to be small compared to the work to be performed. There's little point in spending a second transferring the work if it only takes half a second to do the work.

The job that i have been assigned as a part of my projct is to get the parallel fftw working.. The group where i am working have tons of data that is being gathered day in and day out thru a radio telescope to be processed
Please answer my question about multi-threading and MPI
07-13-2006
kris.c

REgarding the error messages :
.> Writing fftw_init_threads in the code and the library defines fftwInitThreads is one reason why the error message might appear.

Cant agree with u more ..

the lib file that supports multi-threading is " libfftw3l_threads.a "
and its location is : " /compiler/fftw-3.1.1-dp-threads/bin "