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Commit 231b0bbd authored by Uwe Schulzweida's avatar Uwe Schulzweida
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DRMAA update

parent 92561c8c
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src/cdo.c
+ 34
− 10
View file @ 231b0bbd
......@@ -758,10 +758,15 @@ int main(int argc, char *argv[])
{
char commandline[65536];
int i;
int status;
char jobname[1024];
char jobfilename[1024];
FILE *jobfilep;
int ftpget(const char *target, const char *source);
char ftp_url[4096];
char ftpfile[1024];
char tmppath[] = "/localA/m214003/tmp/";
char tmppath2[] = "/scratch/localA/m214003/tmp/";
FILE *jobfilep, *ftpfilep;
int ftpget(int flag, const char *url, const char *path, const char *target, const char *source);
commandline[0] = 0;
strcat(commandline, "/pf/m/m214003/cdt/work/cdo/build/GRID_AMD64/src/cdo ");
......@@ -785,13 +790,13 @@ int main(int argc, char *argv[])
}
fprintf(jobfilep, "#! /bin/bash\n");
fprintf(jobfilep, "uname -s\n");
fprintf(jobfilep, "pwd\n");
fprintf(jobfilep, "ls -l /pf/m/m214003/tmp\n");
fprintf(jobfilep, "cd /scratch/small/m214/m214003/tmp\n");
fprintf(jobfilep, "cd /pf/m/m214003/tmp\n");
fprintf(jobfilep, "#uname -s\n");
fprintf(jobfilep, "#pwd\n");
fprintf(jobfilep, "#ls -l %s\n", tmppath2);
fprintf(jobfilep, "rm -f %s*\n", tmppath2);
fprintf(jobfilep, "cd %s\n", tmppath2);
fprintf(jobfilep, "rm -f %s\n", cdojobfiles);
fprintf(jobfilep, "echo $LD_LIBRARY_PATH\n");
fprintf(jobfilep, "#echo $LD_LIBRARY_PATH\n");
fprintf(jobfilep, "setenv LD_LIBRARY_PATH /opt/gridware/sge/lib/lx24-amd64:$LD_LIBRARY_PATH\n");
fprintf(jobfilep, "%s\n", commandline);
......@@ -801,10 +806,29 @@ int main(int argc, char *argv[])
job_submit(cdoExpName, jobfilename, jobname);
sprintf(commandline, "rm -r %s\n", jobfilename);
sprintf(commandline, "rm -f %s\n", jobfilename);
system(commandline);
ftpget(cdojobfiles, cdojobfiles);
sprintf(commandline, "rm -f %s\n", cdojobfiles);
system(commandline);
sprintf(ftp_url, "ftp://%s.zmaw.de", cdoExpName);
status = ftpget(0, ftp_url, tmppath, cdojobfiles, cdojobfiles);
if ( status == 0 )
{
ftpfilep = fopen(cdojobfiles, "r");
if ( ftpfilep )
{
while ( fscanf(ftpfilep, "%s\n", ftpfile) == 1 )
{
ftpget(1, ftp_url, tmppath, ftpfile, ftpfile);
}
fclose(ftpfilep);
}
}
}
else
{
......
src/job.c
+ 227
− 81
View file @ 231b0bbd
......@@ -3,6 +3,10 @@
#include <string.h>
#include <stdlib.h>
#include <sys/types.h> /* fstat */
#include <sys/stat.h>
#include <unistd.h>
#include "cdo.h"
#if defined (HAVE_LIBDRMAA)
......@@ -40,9 +44,10 @@ static drmaa_job_template_t *create_job_template(const char *expname, const char
/* determine current path */
size = pathconf(".", _PC_PATH_MAX);
if ((dir = (char *)malloc((size_t)size)) != NULL) {
ptr = getcwd(dir, (size_t)size);
}
if ( (dir = (char *)malloc((size_t)size)) != NULL )
{
ptr = getcwd(dir, (size_t)size);
}
/* generate DRMAA conform output path */
......@@ -80,7 +85,7 @@ static drmaa_job_template_t *create_job_template(const char *expname, const char
drmaa_set_attribute(job, DRMAA_OUTPUT_PATH, output_path, NULL, 0);
/* join output/error file */
drmaa_set_attribute(job, DRMAA_JOIN_FILES, "y", NULL, 0);
drmaa_set_attribute(job, DRMAA_JOIN_FILES, "n", NULL, 0);
/* transfer files */
drmaa_set_attribute(job, DRMAA_TRANSFER_FILES, "ieo", NULL, 0);
......@@ -110,41 +115,94 @@ static drmaa_job_template_t *create_job_template(const char *expname, const char
static int drmaa_submit(const char *expname, const char *jobfilename, const char *jobname)
{
char status[DRMAA_ERROR_STRING_BUFFER];
char jobid[DRMAA_JOBNAME_BUFFER], jobout[DRMAA_JOBNAME_BUFFER];
int drmaa_errno, stat;
drmaa_job_template_t *job;
int aborted, exited, signaled, exit_status;
drmaa_attr_values_t *rusage = NULL;
char usage[DRMAA_ERROR_STRING_BUFFER];
int stdout_is_tty = 0;
int errnum;
if (drmaa_init(NULL, status, sizeof(status)-1) != DRMAA_ERRNO_SUCCESS) {
fprintf(stderr, "drmaa_init() failed: %s\n", status);
return 1;
{ /* check character device on stdout */
struct stat statbuf;
fstat(1, &statbuf);
if ( S_ISCHR(statbuf.st_mode) ) stdout_is_tty = 1;
}
if ( drmaa_init(NULL, status, sizeof(status)-1) != DRMAA_ERRNO_SUCCESS )
{
fprintf(stderr, "drmaa_init() failed: %s\n", status);
return 1;
}
/* submit some sequential jobs */
if (!(job = create_job_template(expname, jobfilename, jobname))) {
fprintf(stderr, "create_job_template() failed\n");
return 1;
}
if ( !(job = create_job_template(expname, jobfilename, jobname)) )
{
fprintf(stderr, "create_job_template() failed\n");
return 1;
}
while ((drmaa_errno = drmaa_run_job(jobid, sizeof(jobid)-1, job, status,
sizeof(status)-1)) == DRMAA_ERRNO_DRM_COMMUNICATION_FAILURE) {
fprintf(stderr, "drmaa_run_job() failed - retry: %s\n", status);
sleep(1);
}
if (drmaa_errno != DRMAA_ERRNO_SUCCESS) {
fprintf(stderr, "drmaa_run_job() failed: %s\n", status);
return 1;
}
fprintf(stderr, "job %s submitted.\n", jobid);
while ( (drmaa_errno = drmaa_run_job(jobid, sizeof(jobid)-1, job, status, sizeof(status)-1))
== DRMAA_ERRNO_DRM_COMMUNICATION_FAILURE )
{
fprintf(stderr, "drmaa_run_job() failed - retry: %s\n", status);
sleep(1);
}
if ( drmaa_errno != DRMAA_ERRNO_SUCCESS )
{
fprintf(stderr, "drmaa_run_job() failed: %s\n", status);
return 1;
}
if ( stdout_is_tty )
{
fprintf(stdout, "%s job %s ", expname, jobid);
fprintf(stdout, "submitted");
fflush(stdout);
}
if ( stdout_is_tty )
{
while ( 1 )
{
sleep (1);
errnum = drmaa_job_ps(jobid, &stat, status, DRMAA_ERROR_STRING_BUFFER);
if ( errnum != DRMAA_ERRNO_SUCCESS ) break;
if ( stat == DRMAA_PS_QUEUED_ACTIVE ||
stat == DRMAA_PS_SYSTEM_ON_HOLD ||
stat == DRMAA_PS_USER_ON_HOLD ||
stat == DRMAA_PS_USER_SYSTEM_ON_HOLD )
{
fprintf(stdout, "\b\b\b\b\b\b\b\b\bqueued ");
fflush(stdout);
}
else
break;
}
while ( 1 )
{
sleep (1);
errnum = drmaa_job_ps(jobid, &stat, status, DRMAA_ERROR_STRING_BUFFER);
if ( errnum != DRMAA_ERRNO_SUCCESS ) break;
if ( stat == DRMAA_PS_RUNNING )
{
fprintf(stdout, "\b\b\b\b\b\b\b\b\brunning ");
fflush(stdout);
}
else
break;
}
}
drmaa_delete_job_template(job, NULL, 0);
......@@ -153,34 +211,49 @@ static int drmaa_submit(const char *expname, const char *jobfilename, const char
drmaa_errno = drmaa_wait(jobid, jobout, sizeof(jobout)-1,
&stat, DRMAA_TIMEOUT_WAIT_FOREVER, &rusage, status, sizeof(status)-1);
if (drmaa_errno != DRMAA_ERRNO_SUCCESS) {
fprintf(stderr, "drmaa_wait(%s) failed: %s\n", jobout, status);
return 1;
}
if ( drmaa_errno != DRMAA_ERRNO_SUCCESS )
{
fprintf(stderr, "drmaa_wait(%s) failed: %s\n", jobout, status);
return 1;
}
/*
* report how job finished
*/
drmaa_wifaborted(&aborted, stat, NULL, 0);
if (aborted) {
printf("job %s never ran\n", jobid);
} else {
drmaa_wifexited(&exited, stat, NULL, 0);
if (exited) {
drmaa_wexitstatus(&exit_status, stat, NULL, 0);
printf("job %s finished regularly with exit status %d\n",
jobid, exit_status);
} else {
drmaa_wifsignaled(&signaled, stat, NULL, 0);
if (signaled) {
char termsig[DRMAA_SIGNAL_BUFFER+1];
drmaa_wtermsig(termsig, DRMAA_SIGNAL_BUFFER, stat, NULL, 0);
printf("job %s finished due to signal %s\n", jobid, termsig);
} else
printf("job %s finished with unclear conditions\n", jobid);
if ( aborted )
{
fprintf(stderr, "job %s never ran\n", jobid);
}
}
else
{
drmaa_wifexited(&exited, stat, NULL, 0);
if ( exited )
{
drmaa_wexitstatus(&exit_status, stat, NULL, 0);
if ( stdout_is_tty )
{
fprintf(stdout, "\b\b\b\b\b\b\b\b\bfinished\n");
}
if ( exit_status )
fprintf(stdout, "%s job %s exit status %d\n", expname, jobid, exit_status);
}
else
{
drmaa_wifsignaled(&signaled, stat, NULL, 0);
if ( signaled )
{
char termsig[DRMAA_SIGNAL_BUFFER+1];
drmaa_wtermsig(termsig, DRMAA_SIGNAL_BUFFER, stat, NULL, 0);
fprintf(stderr, "job %s finished due to signal %s\n", jobid, termsig);
}
else
fprintf(stderr, "job %s finished with unclear conditions\n", jobid);
}
}
if ( stdout_is_tty ) fprintf(stdout, "\n");
if ( cdoVerbose )
{
......@@ -193,19 +266,22 @@ static int drmaa_submit(const char *expname, const char *jobfilename, const char
drmaa_release_attr_values (rusage);
if (drmaa_exit(status, sizeof(status)-1) != DRMAA_ERRNO_SUCCESS) {
fprintf(stderr, "drmaa_exit() failed: %s\n", status);
return 1;
}
if ( drmaa_exit(status, sizeof(status)-1) != DRMAA_ERRNO_SUCCESS )
{
fprintf(stderr, "drmaa_exit() failed: %s\n", status);
return 1;
}
{
char commandline[1024];
sprintf(commandline, "cat %s.o%s | grep -v tty | grep -v cannot | grep -v resize | grep -v shell\n", jobname, jobid);
sprintf(commandline, "cat %s.o%s | grep -v tty | grep -v shell\n", jobname, jobid);
system(commandline);
sprintf(commandline, "cat %s.e%s | grep -v cannot | grep -v resize | grep -v rm\n", jobname, jobid);
system(commandline);
sprintf(commandline, "rm -f %s.o%s\n", jobname, jobid);
sprintf(commandline, "rm -f %s.o%s %s.e%s\n", jobname, jobid, jobname, jobid);
system(commandline);
}
......@@ -238,6 +314,7 @@ struct FtpFile {
FILE *stream;
};
int my_fwrite(void *buffer, size_t size, size_t nmemb, void *stream)
{
struct FtpFile *out=(struct FtpFile *)stream;
......@@ -250,18 +327,60 @@ int my_fwrite(void *buffer, size_t size, size_t nmemb, void *stream)
}
int ftpget(const char *target, const char *source)
int my_progress_func(int *stdout_is_tty,
double t, /* dltotal */
double d, /* dlnow */
double ultotal,
double ulnow)
{
if ( *stdout_is_tty )
{
fprintf(stdout, "\b\b\b\b\b%4d%%", (int) (d*100/t));
fflush(stdout);
}
return 0;
}
int ftpget(int flag, const char *url, const char *path, const char *target, const char *source)
{
#if defined (HAVE_LIBCURL)
CURL *curl;
CURLcode res;
struct curl_slist* commands = NULL ;
struct FtpFile ftpfile={
NULL, /* name to store the file as if succesful */
NULL
};
char filename[8196] = "ftp://qftps.zmaw.de/pf/m/m214003/tmp/";
char filename[8196];
char ftpcommand[1024];
char errorbuffer[CURL_ERROR_SIZE];
int status = 0;
int stdout_is_tty = 0;
char prompt[1024];
{ /* check character device on stdout */
struct stat statbuf;
fstat(1, &statbuf);
if ( S_ISCHR(statbuf.st_mode) ) stdout_is_tty = 1;
}
strcat(filename, source);
sprintf(filename, "%s%s", path, source);
sprintf(ftpcommand, "PWD");
commands = curl_slist_append(commands, ftpcommand) ;
sprintf(ftpcommand, "DELE %s\n", filename);
commands = curl_slist_append(commands, ftpcommand) ;
sprintf(filename, "%s%s%s", url, path, source);
if ( flag )
{
sprintf(prompt, "Download %-40s ", filename);
fprintf(stdout, "%s ", prompt);
}
ftpfile.filename = target;
......@@ -269,46 +388,73 @@ int ftpget(const char *target, const char *source)
curl = curl_easy_init();
if(curl) {
curl_easy_setopt(curl, CURLOPT_NETRC, CURL_NETRC_REQUIRED);
if ( curl )
{
curl_easy_setopt(curl, CURLOPT_NETRC, CURL_NETRC_REQUIRED);
curl_easy_setopt(curl, CURLOPT_VERBOSE, 1L);
if ( cdoVerbose )
curl_easy_setopt(curl, CURLOPT_VERBOSE, 1L);
else
curl_easy_setopt(curl, CURLOPT_VERBOSE, 0L);
curl_easy_setopt(curl, CURLOPT_FTP_SSL, CURLFTPSSL_CONTROL);
curl_easy_setopt(curl, CURLOPT_FTPSSLAUTH, CURLFTPAUTH_TLS);
if ( flag )
{
curl_easy_setopt(curl, CURLOPT_NOPROGRESS, FALSE);
curl_easy_setopt(curl, CURLOPT_PROGRESSFUNCTION, my_progress_func);
curl_easy_setopt(curl, CURLOPT_PROGRESSDATA, &stdout_is_tty);
}
curl_easy_setopt(curl, CURLOPT_SSL_VERIFYPEER, 0L);
curl_easy_setopt(curl, CURLOPT_SSL_VERIFYHOST, 0L);
curl_easy_setopt(curl, CURLOPT_FTP_SSL, CURLFTPSSL_CONTROL);
curl_easy_setopt(curl, CURLOPT_FTPSSLAUTH, CURLFTPAUTH_TLS);
curl_easy_setopt(curl, CURLOPT_SSLKEYPASSWD, "");
curl_easy_setopt(curl, CURLOPT_SSL_VERIFYPEER, 0L);
curl_easy_setopt(curl, CURLOPT_SSL_VERIFYHOST, 0L);
curl_easy_setopt(curl, CURLOPT_URL, filename);
curl_easy_setopt(curl, CURLOPT_SSLKEYPASSWD, "");
/* define callback */
curl_easy_setopt(curl, CURLOPT_URL, filename);
curl_easy_setopt(curl, CURLOPT_WRITEFUNCTION, my_fwrite);
/* define callback */
/* set a pointer to struct to pass to the callback */
curl_easy_setopt(curl, CURLOPT_WRITEFUNCTION, my_fwrite);
curl_easy_setopt(curl, CURLOPT_WRITEDATA, &ftpfile);
/* set a pointer to struct to pass to the callback */
res = curl_easy_perform(curl);
curl_easy_setopt(curl, CURLOPT_WRITEDATA, &ftpfile);
curl_easy_cleanup(curl);
curl_easy_setopt(curl, CURLOPT_ERRORBUFFER, errorbuffer);
if(CURLE_OK != res) {
fprintf(stderr, "curl told us %d\n", res);
}
curl_easy_setopt(curl, CURLOPT_POSTQUOTE, commands);
}
res = curl_easy_perform(curl);
if(ftpfile.stream)
fclose(ftpfile.stream);
curl_slist_free_all(commands);
curl_easy_cleanup(curl);
if ( CURLE_OK != res )
{
if ( flag )
{
/* fprintf(stderr, "curl told us %d\n", res); */
fprintf(stderr, "%s\n", errorbuffer);
}
status = -2;
}
}
else
{
status = -1;
}
if ( ftpfile.stream ) fclose(ftpfile.stream);
curl_global_cleanup();
if ( flag ) fprintf(stdout, "\n");
#else
fprintf(stderr, "CURL library not available!\n");
#endif
return 0;
return (status);
}
src/pstream.c
+ 17
− 2
View file @ 231b0bbd
......@@ -494,8 +494,23 @@ int pstreamOpenRead(const char *argument)
else
{
len = strlen(argument);
filename = (char *) malloc(len+1);
strcpy(filename, argument);
if ( cdoExpMode == CDO_EXP_REMOTE )
{
char datapath[] = "/scratch/localA/m214003/data/";
len += strlen(datapath);
filename = (char *) malloc(len+1);
strcpy(filename, datapath);
strcat(filename, argument);
}
else
{
filename = (char *) malloc(len+1);
strcpy(filename, argument);
}
}
if ( PSTREAM_Debug ) Message(func, "file %s", filename);
......
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