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Subject: Re: [OMPI users] MPI_AllGather null terminator character
From: Gabriele Fatigati (g.fatigati_at_[hidden])
Date: 2012-01-27 04:03:02


Sorry,

this is the right code.

2012/1/27 Gabriele Fatigati <g.fatigati_at_[hidden]>

> Hi Jeff,
>
> The problem is when I use strcmp on ALLGather buffer and Valgrind that
> raise a warning.
>
> Please check if the attached code is right, where size(local_hostname) is
> very small.
>
> Valgrind is used as:
>
> mpirun valgrind --leak-check=full --tool=memcheck ./all_gather
>
> and openmpi/1.4.4 compiled with "-O0 -g"
>
> Thanks!
>
> 2012/1/26 Jeff Squyres <jsquyres_at_[hidden]>
>
>> I'm not sure what you're asking.
>>
>> The entire contents of hostname[] will be sent -- from position 0 to
>> position (MAX_STRING_LEN-1). If there's a \0 in there, it will be sent.
>> If the \0 occurs after that, then it won't.
>>
>> Be aware that get_hostname(buf, size) will not put a \0 in the buffer if
>> the hostname is exactly "size" bytes. So you might want to double check
>> that your get_hostname() is returning a \0-terminated string.
>>
>> Does that make sense?
>>
>> Here's a sample I wrote to verify this:
>>
>> #include <stdio.h>
>> #include <string.h>
>> #include <mpi.h>
>> #include <stdlib.h>
>>
>> #define MAX_LEN 64
>>
>> static void where_null(char *ptr, int len, int rank)
>> {
>> int i;
>>
>> for (i = 0; i < len; ++i) {
>> if ('\0' == ptr[i]) {
>> printf("Rank %d: Null found at position %d (string: %s)\n",
>> rank, i, ptr);
>> return;
>> }
>> }
>>
>> printf("Rank %d: Null not found! (string: ", rank);
>> for (i = 0; i < len; ++i) putc(ptr[i], stdout);
>> putc('\n', stdout);
>> }
>>
>> int main()
>> {
>> int i;
>> char hostname[MAX_LEN];
>> char *hostname_recv_buf;
>> int rank, size;
>>
>> MPI_Init(NULL, NULL);
>> MPI_Comm_rank(MPI_COMM_WORLD, &rank);
>> MPI_Comm_size(MPI_COMM_WORLD, &size);
>>
>> gethostname(hostname, MAX_LEN - 1);
>> where_null(hostname, MAX_LEN, rank);
>>
>> hostname_recv_buf = calloc(size * (MAX_LEN), (sizeof(char)));
>> MPI_Allgather(hostname, MAX_LEN, MPI_CHAR,
>> hostname_recv_buf, MAX_LEN, MPI_CHAR, MPI_COMM_WORLD);
>> for (i = 0; i < size; ++i) {
>> where_null(hostname_recv_buf + i * MAX_LEN, MAX_LEN, rank);
>> }
>>
>> MPI_Finalize();
>> return 0;
>> }
>>
>>
>>
>> On Jan 13, 2012, at 2:32 AM, Gabriele Fatigati wrote:
>>
>> > Dear OpenMPI,
>> >
>> > using MPI_Allgather with MPI_CHAR type, I have a doubt about
>> null-terminated character. Imaging I want to spawn node names where my
>> program is running on:
>> >
>> >
>> > ----------------------------------------
>> >
>> > char hostname[MAX_LEN];
>> >
>> > char*
>> hostname_recv_buf=(char*)calloc(num_procs*(MAX_STRING_LEN),(sizeof(char)));
>> >
>> > MPI_Allgather(hostname, MAX_STRING_LEN, MPI_CHAR, hostname_recv_buf,
>> MAX_STRING_LEN, MPI_CHAR, MPI_COMM_WORLD);
>> >
>> > ----------------------------------------
>> >
>> >
>> > Now, is the null-terminated character of each local string included? Or
>> I have to send and receive in MPI_Allgather MAX_STRING_LEN+1 elements?
>> >
>> > Using Valgrind, in a subsequent simple strcmp:
>> >
>> > for( i= 0; i< num_procs; i++){
>> > if(strcmp(&hostname_recv_buf[MAX_STRING_LEN*i],
>> local_hostname)==0){
>> > ... doing something....
>> > }
>> > }
>> >
>> > raise a warning:
>> >
>> > Conditional jump or move depends on uninitialised value(s)
>> > ==19931== at 0x4A06E5C: strcmp (mc_replace_strmem.c:412)
>> >
>> > The same warning is not present if I use MAX_STRING_LEN+1 in
>> MPI_Allgather.
>> >
>> >
>> > Thanks in forward.
>> >
>> > --
>> > Ing. Gabriele Fatigati
>> >
>> > HPC specialist
>> >
>> > SuperComputing Applications and Innovation Department
>> >
>> > Via Magnanelli 6/3, Casalecchio di Reno (BO) Italy
>> >
>> > www.cineca.it Tel: +39 051 6171722
>> >
>> > g.fatigati [AT] cineca.it
>> > _______________________________________________
>> > users mailing list
>> > users_at_[hidden]
>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> --
>> Jeff Squyres
>> jsquyres_at_[hidden]
>> For corporate legal information go to:
>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>
>
>
> --
> Ing. Gabriele Fatigati
>
> HPC specialist
>
> SuperComputing Applications and Innovation Department
>
> Via Magnanelli 6/3, Casalecchio di Reno (BO) Italy
>
> www.cineca.it Tel: +39 051 6171722
>
> g.fatigati [AT] cineca.it
>

-- 
Ing. Gabriele Fatigati
HPC specialist
SuperComputing Applications and Innovation Department
Via Magnanelli 6/3, Casalecchio di Reno (BO) Italy
www.cineca.it                    Tel:   +39 051 6171722
g.fatigati [AT] cineca.it