MySQL Bugs: #30311: ERROR 2013 (HY000): Lost connection to MySQL server during query

Bug #30311	ERROR 2013 (HY000): Lost connection to MySQL server during query
Submitted:	8 Aug 2007 14:55	Modified:	6 Jan 2008 10:20
Reporter:	Aurélie de LUCA	Email Updates:
Status:	No Feedback	Impact on me:	None
Category:	MySQL Server	Severity:	S3 (Non-critical)
Version:	5.0.32-Debian_7etch1-log	OS:	Linux
Assigned to:	Assigned Account	CPU Architecture:	Any

Description:
Hello, 

I have write an UDF whose code functions when I call it in a program main, but which turns over the error when I call it in MySQL : 

ERROR 2013 (HY000): Lost connection to MySQL server during query.

I looked at bugs preceding, but my database is in MyISAM and I have all the rights root.

You have the UDF code which is composed of a C code, of a wrapper and of a C++ code below:

C code :

my_bool fingerprint_init(UDF_INIT *initid, UDF_ARGS *args, char *message)
{
  if (args->arg_count != 2 || args->arg_type[0] != STRING_RESULT && args->arg_type[1] != STRING_RESULT)
  {
    strcpy(message,"Usage: FunctionName (InputFileName,FPTType)");
    return 1;
  }
 return 0;
}

void fingerprint_deinit(UDF_INIT *initid)
{}

char *fingerprint(UDF_INIT *initid, UDF_ARGS *args, char *result, unsigned long *length, char *is_null, char *error)
{
  //char *b = malloc(2*sizeof(char));
  //b = result;
  char *molfile = args->args[0];
  char *output;
  char *e = args->args[1];

  result = conversionfpt(molfile,e);
  output = strdup(result);
  *length=strlen(output);

  return output;

}

wrapper :

char *conversionfpt(char *molfile, char *type);

C++ code :

char *conversionfpt(char * molfile, char *type)
{
  int i;
  string f;
  string mode(type);
  char *e;
  istringstream ist(molfile);
  OBMol mol;
  OBConversion conv;
  OBFingerprint *fingerprint;
  vector < unsigned int >vfp;

  fingerprint = OBFingerprint::FindFingerprint ("FP2");

  conv.Read (&mol, &ist);

  fingerprint->GetFingerprint (&mol, vfp);

  char b[(vfp.size () * sizeof(unsigned int))];
 
  for (i = 0; i< vfp.size(); i++) sprintf(&b[i],"%ld",vfp[i]);
  e = strdup(b);

  return e;
}

Thank you for your help.

Aurélie

How to repeat:
aureliedeluca@gmail.com

Thank you for the bug report. The version reported is pretty older, could
you please test with the latest released version 5.0.45. Thanks in advance.

Hello, 

It is impossible for me to install version 5.0.45 because the person responsible for computer equipement is on holiday. I make only development. I tested all the day install version 5.0.45 but I could not arrive, and I must regulate this problem of UDF at all costs. I notice that I could install another UDF with version 5.0.32 and I did not have this type of problem. 

How to make it, please, without installing the 5.0.45? 

Thank you in advance.

Well, if it works with another UDF, than the problem could be in your UDF.
Try to find where a crash happens. For example make mysqld to dump core and look at the core dump. Or add debug printf()'s to your UDF.

Hello,

I have to listen to you, and I tried to install 5.0.45, but today I cannot use my FindMySQL.cmake any more. I have the following error, it does not find mysqlclient. However it is well to install since I reinstalled my starting version. I however specify the way to him or to find it, but it does not find the bookshop which definite args for example. Must I install something of other?

Thank you in advance.

PS: By using a file.sql and a request bash, I could install my UDF.

I have found what install in order to make function my FoundMySQL.cmake. I needed the mysql++ package. 

Thank you for all.

Aurélie

Thank you for the feedback.

Does last comment mean bug is not repeatble if you use mysql++?

No, I badly expressed myself. The bug disappears if I use a file.sql to add my UDF in the table mysql. I can then use my UDF without problems in my tables. 
I don't understand, because they are the same orders as that typed in mysql but all sets in a file.sql that I send to mysql by a request of the type:

mysql -u root -p mysql < file.mysql

Aurélie

Thank you for the feedback.

Please provide file file.sql

No feedback was provided for this bug for over a month, so it is
being suspended automatically. If you are able to provide the
information that was originally requested, please do so and change
the status of the bug back to "Open".

SQL request

Attachment: mychem.sql (application/octet-stream, text), 2.70 KiB.

Hello,

Excuse me, I had a problem to connect me. But I have sent my file file.sql that you can download in Files.

Cheers.

Aurélie

Thank you for the feedback.

Please also provide your error log file with records made in time when you get Lost connection error.

No feedback was provided for this bug for over a month, so it is
being suspended automatically. If you are able to provide the
information that was originally requested, please do so and change
the status of the bug back to "Open".