Hi all
We have been using postgreSQL version 8.1.11 for 6 years and have to
move our website to another server recently. We did not manage to get
the version 8.1.11 thus have to use version 8.4.12 in the new server.
This version is still quite old but we cannot make the databases running
in any of newer versions.
We met a problem after running the website for one week. We used a
function to convert and save binary files into the database (as bytea).
This function worked well in the old version but sometimes makes the new
version of postgres crash. This random crash is not file specific.
Sometimes, the function works well in all binary files but makes crashes
again and again at other times.
The OS system in the new server is: Ubuntu 12.04.2.
The error messages are:
2(56608) SELECT: malloc.c:2451: sYSMALLOc: Assertion `(old_top ==
(((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) -
__builtin_offsetof (struct malloc_chunk, fd)))) && old_size == 0) ||
((unsigned long) (old_size) >= (unsigned long)(
(((__builtin_offsetof (struct malloc_chunk, fd_nextsize))+((2 *
(sizeof(size_t))) - 1)) & ~((2 * (sizeof(size_t))) - 1))) &&
((old_top)->size & 0x1) && ((unsigned long)old_end & pagemask) == 0)'
failed.
LOG: server process (PID 8866) was terminated by signal 6: Aborted
LOG: terminating any other active server processes
WARNING: terminating connection because of crash of another server process
DETAIL: The postmaster has commanded this server process to roll back
the current transaction and exit, because another server process exited
abnormally and possibly corrupted shared memory.
HINT: In a moment you should be able to reconnect to the database and
repeat your command.
WARNING: terminating connection because of crash of another server process
DETAIL: The postmaster has commanded this server process to roll back
the current transaction and exit, because another server process exited
abnormally and possibly corrupted shared memory.
HINT: In a moment you should be able to reconnect to the database and
repeat your command.
WARNING: terminating connection because of crash of another server process
DETAIL: The postmaster has commanded this server process to roll back
the current transaction and exit, because another server process exited
abnormally and possibly corrupted shared memory.
HINT: In a moment you should be able to reconnect to the database and
repeat your command.
WARNING: terminating connection because of crash of another server process
DETAIL: The postmaster has commanded this server process to roll back
the current transaction and exit, because another server process exited
abnormally and possibly corrupted shared memory.
HINT: In a moment you should be able to reconnect to the database and
repeat your command.
WARNING: terminating connection because of crash of another server process
DETAIL: The postmaster has commanded this server process to roll back
the current transaction and exit, because another server process exited
abnormally and possibly corrupted shared memory.
HINT: In a moment you should be able to reconnect to the database and
repeat your command.
WARNING: terminating connection because of crash of another server process
DETAIL: The postmaster has commanded this server process to roll back
the current transaction and exit, because another server process exited
abnormally and possibly corrupted shared memory.
HINT: In a moment you should be able to reconnect to the database and
repeat your command.
WARNING: terminating connection because of crash of another server process
DETAIL: The postmaster has commanded this server process to roll back
the current transaction and exit, because another server process exited
abnormally and possibly corrupted shared memory.
HINT: In a moment you should be able to reconnect to the database and
repeat your command.
LOG: all server processes terminated; reinitializing
LOG: database system was interrupted; last known up at 2014-05-26
10:53:57 BST
LOG: database system was not properly shut down; automatic recovery in
progress
LOG: redo starts at 1/D2BC56A0
LOG: record with zero length at 1/D2BCC600
LOG: redo done at 1/D2BCC5C8
LOG: last completed transaction was at log time 2014-05-26
11:31:07.172215+01
LOG: database system is ready to accept connections
LOG: autovacuum launcher started
And here is the C function, which was written at about 10 years ago and
was compiled by "gcc -O2 -shared -fPIC convert_bin_to_64.c -o
convert_bin_to_64.so".
#include "postgres.h"
#include "fmgr.h"
#include <string.h>
PG_MODULE_MAGIC;
bytea *convert_bin_to_64(bytea *t)
/* unsingned char weil Sonderzeichen auch negativ sein k?nnen*/
{
int ps,v0,v1,v2,v3,vl,ps2;
char charset[70];
int size=VARSIZE(t)-VARHDRSZ; /* VARSIZE and VARHDRSZ are
PostgreSql Macros*/
bytea *result = (bytea *)
palloc(VARHDRSZ+sizeof(char)*(4*(size)/3+15));
strcpy(charset,"abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789%*");
sprintf(((unsigned char*) VARDATA(result)),"B64D%.10d",size);
ps2=14;
for (ps=0; ps<size;ps+=3)
{
v0=0;if (ps+0<size) v0=*((unsigned char*)(VARDATA(t)+ps+0));
v1=0;if (ps+1<size) v1=*((unsigned char*)(VARDATA(t)+ps+1));
v2=0;if (ps+2<size) v2=*((unsigned char*)(VARDATA(t)+ps+2));
vl=v0+(v1+v2*256)*256;
v0=vl%64;vl>>=6; /*vl=vl/64;*/
v1=vl%64;vl>>=6;
v2=vl%64;vl>>=6;
v3=vl%64;
*((unsigned char*)(VARDATA(result)+ps2))=charset[v0];
*((unsigned char*)(VARDATA(result)+ps2+1))=charset[v1];
*((unsigned char*)(VARDATA(result)+ps2+2))=charset[v2];
*((unsigned char*)(VARDATA(result)+ps2+3))=charset[v3];
ps2+=4;
}
*((unsigned char*)(VARDATA(result)+ps2))=0;
SET_VARSIZE(result, ps2 + VARHDRSZ);
/* VARATT_SIZEP(result) << ps2+VARHDRSZ;*/
return result;
}
Thanks
Zhemin
--
Zhemin Zhou
Bioinformatician
