wxBitmap* CSimpleProjectPanel::GetProjectSpecificBitmap(char* project_url) {
char defaultIcnPath[256];
CSkinSimple* pSkinSimple = wxGetApp().GetSkinManager()->GetSimple();
wxASSERT(pSkinSimple);
// Only update it if project specific is found
if(boinc_resolve_filename(GetProjectIconLoc(project_url).c_str(), defaultIcnPath, sizeof(defaultIcnPath)) == 0) {
wxBitmap* projectBM;
wxString strIconPath = wxString(defaultIcnPath,wxConvUTF8);
if (wxFile::Exists(strIconPath)) {
#ifdef __WXMSW__
if ((GetXDPIScaling() > 1.05) || (GetYDPIScaling() > 1.05)) {
wxImage img = wxImage(strIconPath, wxBITMAP_TYPE_ANY);
if (img.IsOk()) {
img.Rescale((int) (img.GetWidth()*GetXDPIScaling()),
(int) (img.GetHeight()*GetYDPIScaling()),
wxIMAGE_QUALITY_BILINEAR
);
projectBM = new wxBitmap(img);
if (projectBM->IsOk()) {
return projectBM;
}
}
} else
#endif
{
projectBM = new wxBitmap();
if ( projectBM->LoadFile(strIconPath, wxBITMAP_TYPE_ANY) ) {
return projectBM;
}
}
}
}
return pSkinSimple->GetProjectImage()->GetBitmap();
}
int main(int argc, char **argv) {
int retval;
double fd;
char output_path[512]; //, chkpt_path[512];
//FILE* state;
retval = boinc_init();
if (retval) {
fprintf(stderr, "boinc_init returned %d\n", retval);
exit(retval);
}
// extract a --device option
std::vector<char*> argVec;
int cudaDevice = -1;
for(int ii = 0; ii < argc; ii++) {
if(cudaDevice < 0 && strcmp(argv[ii], "--device") == 0 && ii + 1 < argc)
cudaDevice = atoi(argv[++ii]);
else
argVec.push_back(argv[ii]);
}
argc = (int)argVec.size();
argv = &argVec[0];
if(cudaDevice < 0)
cudaDevice = 0;
boinc_begin_critical_section();
// set the cuda device
if ( rcuda::SetCudaDevice(cudaDevice) != 0 ) {
fprintf(stderr, "Error setting device %u. Temporary exiting for 60 secs\n", cudaDevice);
boinc_temporary_exitHack();
}
cudaDeviceProp deviceProp;
if(cudaGetDeviceProperties(&deviceProp, cudaDevice) == cudaErrorInvalidDevice) {
fprintf(stderr, "Error querying device %u. Temporary exiting for 60 secs\n", cudaDevice);
boinc_temporary_exitHack();
}
#ifdef WIN32
SetThreadPriority(GetCurrentThread(), THREAD_PRIORITY_ABOVE_NORMAL);
#endif
int buffCount = 0x2000;
int chainSize = 100;
if(deviceProp.major == 1) {
/*
buffCount = deviceProp.multiProcessorCount * 8;// 8 blocks per multiprocessor
buffCount *= deviceProp.maxThreadsPerBlock / 64; // (BLOCK_X_SIZE)
// buffCount *= 24;
if(deviceProp.minor <= 1) buffCount *= 24; // 24 warps per multiprocessor for compute 1.0 and 1.1
else buffCount *= 32; // 32 warps per multiprocessor for compute 1.2 and 1.3
*/
buffCount = 0x2000;
}
else if(deviceProp.major == 2) {
chainSize = 200;
/* buffCount = deviceProp.multiProcessorCount * 8;// 8 blocks per multiprocessor
buffCount *= deviceProp.maxThreadsPerBlock / 64; //(BLOCK_X_SIZE)
buffCount *= 32; // 48 warps per multiprocessor for compute 2.x
/* if(deviceProp.minor == 1) {
buffCount *= 2;
}
*/
buffCount = 0x4000;
}
if(cudaDevice > 0) {
chainSize = 1000;
}
if(argc < 10)
{
fprintf(stderr, "Not enough parameters");
return -1;
}
std::string sHashRoutineName, sCharsetName, sSalt, sCheckPoints;
uint32 nRainbowChainCount, nPlainLenMin, nPlainLenMax, nRainbowTableIndex, nRainbowChainLen;
uint64 nChainStart;
sHashRoutineName = argv[1];
sCharsetName = argv[2];
nPlainLenMin = atoi(argv[3]);
nPlainLenMax = atoi(argv[4]);
nRainbowTableIndex = atoi(argv[5]);
nRainbowChainLen = atoi(argv[6]);
nRainbowChainCount = atoi(argv[7]);
#ifdef _WIN32
nChainStart = _atoi64(argv[8]);
#else
nChainStart = atoll(argv[8]);
#endif
sCheckPoints = argv[9];
std::vector<int> vCPPositions;
char *cp = strtok((char *)sCheckPoints.c_str(), ",");
while(cp != NULL)
{
vCPPositions.push_back(atoi(cp));
cp = strtok(NULL, ",");
}
if(argc == 11)
{
sSalt = argv[10];
}
//std::cout << "Starting ChainGenerator" << std::endl;
// Setup CChainWalkContext
//std::cout << "ChainGenerator started." << std::endl;
if (!CChainWalkContext::SetHashRoutine(sHashRoutineName))
{
fprintf(stderr, "hash routine %s not supported\n", sHashRoutineName.c_str());
return 1;
}
//std::cout << "Hash routine validated" << std::endl;
if (!CChainWalkContext::SetPlainCharset(sCharsetName, nPlainLenMin, nPlainLenMax))
{
std::cerr << "charset " << sCharsetName << " not supported" << std::endl;
return 2;
}
//std::cout << "Plain charset validated" << std::endl;
if (!CChainWalkContext::SetRainbowTableIndex(nRainbowTableIndex))
{
std::cerr << "invalid rainbow table index " << nRainbowTableIndex << std::endl;
return 3;
}
//std::cout << "Rainbowtable index validated" << std::endl;
if(sHashRoutineName == "mscache")// || sHashRoutineName == "lmchall" || sHashRoutineName == "halflmchall")
{
// Convert username to unicode
const char *szSalt = sSalt.c_str();
int salt_length = strlen(szSalt);
unsigned char cur_salt[256];
for (int i=0; i<salt_length; i++)
{
cur_salt[i*2] = szSalt[i];
cur_salt[i*2+1] = 0x00;
}
CChainWalkContext::SetSalt(cur_salt, salt_length*2);
}
else if(sHashRoutineName == "halflmchall")
{ // The salt is hardcoded into the hash routine
// CChainWalkContext::SetSalt((unsigned char*)&salt, 8);
}
else if(sHashRoutineName == "oracle")
{
CChainWalkContext::SetSalt((unsigned char *)sSalt.c_str(), sSalt.length());
}
//std::cout << "Opening chain file" << std::endl;
// Open file
boinc_resolve_filename("result", output_path, sizeof(output_path));
fclose(boinc_fopen(output_path, "a"));
FILE *outfile = boinc_fopen(output_path, "r+b");
if (outfile == NULL)
{
std::cerr << "failed to create " << output_path << std::endl;
return 4;
}
// Check existing chains
unsigned int nDataLen = (unsigned int)GetFileLen(outfile);
// Round to boundary
nDataLen = nDataLen / 10 * 10;
if (nDataLen == nRainbowChainCount * 10)
{
std::cerr << "precomputation of this rainbow table already finished" << std::endl;
fclose(outfile);
return 0;
}
fseek(outfile, nDataLen, SEEK_SET);
//XXX size_t isn't 32/64 clean
size_t nReturn;
CChainWalkContext cwc;
uint64 nIndex[2];
//time_t tStart = time(NULL);
// std::cout << "Starting to generate chains" << std::endl;
int maxCalcBuffSize = rcuda::GetChainsBufferSize( buffCount );
std::cerr << "maxCalcBuffSize - estimated: " << buffCount << ". Chosen: " << maxCalcBuffSize << std::endl;
uint64 *calcBuff = new uint64[2*maxCalcBuffSize];
int ii;
CudaCWCExtender ex(&cwc);
rcuda::RCudaTask cuTask;
ex.Init();
for(int nCurrentCalculatedChains = nDataLen / 10, calcSize; nCurrentCalculatedChains < nRainbowChainCount; )
{
fd = (double)nCurrentCalculatedChains / (double)nRainbowChainCount;
boinc_fraction_done(fd);
cuTask.hash = ex.GetHash();
cuTask.startIdx = nChainStart + nCurrentCalculatedChains;
cuTask.idxCount = std::min<int>(nRainbowChainCount - nCurrentCalculatedChains, maxCalcBuffSize);
cuTask.dimVec = ex.GetPlainDimVec();
cuTask.dimVecSize = ex.GetPlainDimVecSize()/2;
cuTask.charSet = ex.GetCharSet();
cuTask.charSetSize = ex.GetCharSetSize();
cuTask.cpPositions = &vCPPositions[0];
cuTask.cpPosSize = vCPPositions.size();
cuTask.reduceOffset = ex.GetReduceOffset();
cuTask.plainSpaceTotal = ex.GetPlainSpaceTotal();
cuTask.rainbowChainLen = nRainbowChainLen;
cuTask.kernChainSize = chainSize;
for(ii = 0; ii < cuTask.idxCount; ii++) {
calcBuff[2*ii] = cuTask.startIdx + ii;
calcBuff[2*ii+1] = 0;
}
calcSize = rcuda::CalcChainsOnCUDA(&cuTask, calcBuff);
BOINC_STATUS boinc_status;
boinc_get_status(&boinc_status);
if (boinc_status.quit_request || boinc_status.abort_request)
{
boinc_end_critical_section();
while (1) boinc_sleep(1);
}
if(calcSize > 0) {
nCurrentCalculatedChains += calcSize;
for(ii = 0; ii < cuTask.idxCount; ii++) {
nIndex[0] = cuTask.startIdx + ii;
// nReturn = fwrite(nIndex, 1, 8, outfile);
nReturn = fwrite(calcBuff+(2*ii), 1, 8, outfile);
nReturn += fwrite(calcBuff+(2*ii+1), 1, 2, outfile);
if(nReturn != 10) {
std::cerr << "disk write fail" << std::endl;
fclose(outfile);
return 9;
}
}
} else {
std::cerr << "Calculations on CUDA failed!" << std::endl;
fclose(outfile);
return -1;
}
}
delete [] calcBuff;
#ifdef _DEBUG
std::cout << "Generation completed" << std::endl;
#endif
fclose(outfile);
boinc_fraction_done(1);
boinc_finish(0);
}
int main(int argc, char** argv) {
passwd *pw;
group *grp;
char user_name[256], group_name[256];
char gfx_app_path[MAXPATHLEN], resolved_path[MAXPATHLEN];
char *BOINCDatSlotsPath = "/Library/Application Support/BOINC Data/slots/";
int retval;
int pid;
if (argc < 2) return EINVAL;
strlcpy(user_name, "boinc_project", sizeof(user_name));
strlcpy(group_name, user_name, sizeof(group_name));
#if 0 // For debugging only
// Allow debugging without running as user or group boinc_project
pw = getpwuid(getuid());
if (pw) strlcpy(user_name, pw->pw_name, sizeof(user_name));
grp = getgrgid(getgid());
if (grp) strlcpy(group_name, grp->gr_gid, sizeof(group_name));
#endif
// We are running setuid root, so setgid() sets real group ID,
// effective group ID and saved set_group-ID for this process
grp = getgrnam(group_name);
if (grp) setgid(grp->gr_gid);
// We are running setuid root, so setuid() sets real user ID,
// effective user ID and saved set_user-ID for this process
pw = getpwnam(user_name);
if (pw) setuid(pw->pw_uid);
// NOTE: call print_to_log_file only after switching user and group
#if 0 // For debugging only
char current_dir[MAXPATHLEN];
getcwd( current_dir, sizeof(current_dir));
print_to_log_file( "current directory = %s", current_dir);
for (int i=0; i<argc; i++) {
print_to_log_file("switcher arg %d: %s", i, argv[i]);
}
#endif
if (strcmp(argv[1], "-default_gfx") == 0) {
strlcpy(resolved_path, "/Library/Application Support/BOINC Data/boincscr", sizeof(resolved_path));
argv[2] = resolved_path;
#if 0 // For debugging only
for (int i=2; i<argc; i++) {
print_to_log_file("calling execv with arg %d: %s", i-2, argv[i]);
}
#endif
// For unknown reasons, the graphics application exits with
// "RegisterProcess failed (error = -50)" unless we pass its
// full path twice in the argument list to execv.
execv(resolved_path, argv+2);
// If we got here execv failed
fprintf(stderr, "Process creation (%s) failed: errno=%d\n", resolved_path, errno);
return errno;
}
if (strcmp(argv[1], "-launch_gfx") == 0) {
strlcpy(gfx_app_path, BOINCDatSlotsPath, sizeof(gfx_app_path));
strlcat(gfx_app_path, argv[2], sizeof(gfx_app_path));
strlcat(gfx_app_path, "/", sizeof(gfx_app_path));
strlcat(gfx_app_path, GRAPHICS_APP_FILENAME, sizeof(gfx_app_path));
retval = boinc_resolve_filename(gfx_app_path, resolved_path, sizeof(resolved_path));
if (retval) return retval;
argv[2] = resolved_path;
#if 0 // For debugging only
for (int i=2; i<argc; i++) {
print_to_log_file("calling execv with arg %d: %s", i-2, argv[i]);
}
#endif
// For unknown reasons, the graphics application exits with
// "RegisterProcess failed (error = -50)" unless we pass its
// full path twice in the argument list to execv.
execv(resolved_path, argv+2);
// If we got here execv failed
fprintf(stderr, "Process creation (%s) failed: errno=%d\n", resolved_path, errno);
return errno;
}
if (strcmp(argv[1], "-kill_gfx") == 0) {
pid = atoi(argv[2]);
if (! pid) return EINVAL;
if ( kill(pid, SIGKILL)) {
#if 0 // For debugging only
print_to_log_file("kill(%d, SIGKILL) returned error %d", pid, errno);
#endif
return errno;
}
return 0;
}
return EINVAL; // Unknown command
}
void worker() {
int nchars = 0;
int retval;
char input_path[512];
char output_path[512];
FILE* outfile;
FILE *infile;
boinc_resolve_filename(INPUT_FILE, input_path, sizeof(input_path));
#ifdef _WIN32
infile = boinc_fopen(input_path, "rb");
#else
infile = boinc_fopen(input_path, "r");
#endif
if (!infile) {
fprintf(stderr,
"Couldn't find input file, resolved name %s.\n", input_path
);
exit(-1);
}
// Dance Dance Revolution
dfio_load_file(infile);
SBMatrix* matrix = new SBMatrix();
retval = dfio_read_matrix(matrix);
if (retval) {
fprintf(stderr, "APP: bdance parse input file failed:\n");
fprintf(stderr, "error code %d\n", retval);
dfio_cleanup();
exit(1);
}
dfio_cleanup();
fclose(infile);
// Solve
dlx_solve(matrix);
uxlong solutions = dlx_count_solutions();
delete matrix;
// Write results.
boinc_resolve_filename(OUTPUT_FILE, output_path, sizeof(output_path));
outfile = boinc_fopen(output_path, "w");
if (!outfile) {
fprintf(stderr,
"Couldn't find output file, resolved name %s.\n", output_path
);
exit(-1);
}
dfio_new_file(outfile, DFIO_TYPE_RESULT);
// if (dfio_get_prop(DFIO_PROP_NO_SOLUTION_DATA)) {
dfio_set_prop(DFIO_PROP_RESULTS_NUM, solutions);
dfio_write_headers();
// }
dfio_cleanup();
fclose(outfile);
boinc_finish(0);
}
int main(int argc, char **argv) {
int retval;
double fd;
char output_path[512]; //, chkpt_path[512];
//FILE* state;
retval = boinc_init();
if (retval) {
fprintf(stderr, "boinc_init returned %d\n", retval);
exit(retval);
}
// get size of input file (used to compute fraction done)
//
//file_size(input_path, fsize);
// See if there's a valid checkpoint file.
// If so seek input file and truncate output file
//
if(argc < 10)
{
fprintf(stderr, "Not enough parameters");
return -1;
}
std::string sHashRoutineName, sCharsetName, sSalt, sCheckPoints;
uint32 nRainbowChainCount, nPlainLenMin, nPlainLenMax, nRainbowTableIndex, nRainbowChainLen;
uint64 nChainStart;
sHashRoutineName = argv[1];
sCharsetName = argv[2];
nPlainLenMin = atoi(argv[3]);
nPlainLenMax = atoi(argv[4]);
nRainbowTableIndex = atoi(argv[5]);
nRainbowChainLen = atoi(argv[6]);
nRainbowChainCount = atoi(argv[7]);
#ifdef _WIN32
nChainStart = _atoi64(argv[8]);
#else
nChainStart = atoll(argv[8]);
#endif
sCheckPoints = argv[9];
std::vector<uint32> vCPPositions;
char *cp = strtok((char *)sCheckPoints.c_str(), ",");
while(cp != NULL)
{
vCPPositions.push_back(atoi(cp));
cp = strtok(NULL, ",");
}
if(argc == 11)
{
sSalt = argv[10];
}
//std::cout << "Starting ChainGenerator" << std::endl;
// Setup CChainWalkContext
//std::cout << "ChainGenerator started." << std::endl;
if (!CChainWalkContext::SetHashRoutine(sHashRoutineName))
{
fprintf(stderr, "hash routine %s not supported\n", sHashRoutineName.c_str());
return 1;
}
//std::cout << "Hash routine validated" << std::endl;
if (!CChainWalkContext::SetPlainCharset(sCharsetName, nPlainLenMin, nPlainLenMax))
{
std::cerr << "charset " << sCharsetName << " not supported" << std::endl;
return 2;
}
//std::cout << "Plain charset validated" << std::endl;
if (!CChainWalkContext::SetRainbowTableIndex(nRainbowTableIndex))
{
std::cerr << "invalid rainbow table index " << nRainbowTableIndex << std::endl;
return 3;
}
//std::cout << "Rainbowtable index validated" << std::endl;
if(sHashRoutineName == "mscache")// || sHashRoutineName == "lmchall" || sHashRoutineName == "halflmchall")
{
// Convert username to unicode
const char *szSalt = sSalt.c_str();
int salt_length = strlen(szSalt);
unsigned char cur_salt[256];
for (int i=0; i<salt_length; i++)
{
cur_salt[i*2] = szSalt[i];
cur_salt[i*2+1] = 0x00;
}
CChainWalkContext::SetSalt(cur_salt, salt_length*2);
}
else if(sHashRoutineName == "halflmchall")
{ // The salt is hardcoded into the hash routine
// CChainWalkContext::SetSalt((unsigned char*)&salt, 8);
}
else if(sHashRoutineName == "oracle")
{
CChainWalkContext::SetSalt((unsigned char *)sSalt.c_str(), sSalt.length());
}
//std::cout << "Opening chain file" << std::endl;
// Open file
boinc_resolve_filename("result", output_path, sizeof(output_path));
fclose(boinc_fopen(output_path, "a"));
FILE *outfile = boinc_fopen(output_path, "r+b");
if (outfile == NULL)
{
std::cerr << "failed to create " << output_path << std::endl;
return 4;
}
// Check existing chains
unsigned int nDataLen = (unsigned int)GetFileLen(outfile);
// Round to boundary
nDataLen = nDataLen / 10 * 10;
if (nDataLen == nRainbowChainCount * 10)
{
std::cerr << "precomputation of this rainbow table already finished" << std::endl;
fclose(outfile);
return 0;
}
nChainStart += (nDataLen / 10);
fseek(outfile, nDataLen, SEEK_SET);
//XXX size_t isn't 32/64 clean
size_t nReturn;
CChainWalkContext cwc;
uint64 nIndex[2];
//time_t tStart = time(NULL);
// std::cout << "Starting to generate chains" << std::endl;
for(uint32 nCurrentCalculatedChains = nDataLen / 10; nCurrentCalculatedChains < nRainbowChainCount; nCurrentCalculatedChains++)
{
uint32 cpcheck = 0;
unsigned short checkpoint = 0;
fd = (double)nCurrentCalculatedChains / (double)nRainbowChainCount;
boinc_fraction_done(fd);
cwc.SetIndex(nChainStart++); // use a given index now!
nIndex[0] = cwc.GetIndex();
for (uint32 nPos = 0; nPos < nRainbowChainLen - 1; nPos++)
{
// std::cout << "IndexToPlain()" << std::endl;
cwc.IndexToPlain();
// std::cout << "PlainToHash()" << std::endl;
cwc.PlainToHash();
// std::cout << "HashToIndex()" << std::endl;
cwc.HashToIndex(nPos);
if(cpcheck < vCPPositions.size() && nPos == vCPPositions[cpcheck])
{
checkpoint |= (1 << cpcheck) & (unsigned short)cwc.GetIndex() << cpcheck;
cpcheck++;
}
}
//std::cout << "GetIndex()" << std::endl;
nIndex[1] = cwc.GetIndex();
// Write chain to disk
if ((nReturn = fwrite(&nIndex[1], 1, 8, outfile)) != 8)
{
std::cerr << "disk write fail" << std::endl;
fclose(outfile);
return 9;
}
if((nReturn = fwrite(&checkpoint, 1, 2, outfile)) != 2)
{
std::cerr << "disk write fail" << std::endl;
fclose(outfile);
return 9;
}
}
//std::cout << "Generation completed" << std::endl;
fclose(outfile);
boinc_fraction_done(1);
boinc_finish(0);
}
int DC_sendResult(const char *logicalFileName, const char *path,
DC_FileMode mode)
{
char label[32], new_path[PATH_MAX], msg[PATH_MAX], *p;
int ret;
if (!logicalFileName)
{
DC_log(LOG_ERR, "%s: Missing logical file name", __func__);
return DC_ERR_BADPARAM;
}
if (!path)
{
DC_log(LOG_ERR, "%s: Missing path", __func__);
return DC_ERR_BADPARAM;
}
if (!DC_getMaxSubresults())
{
DC_log(LOG_ERR, "No more subresults are allowed to be sent");
return DC_ERR_NOTIMPL;
}
/* We have to use the subresult labels that were defined by the
* master for doing the upload */
snprintf(label, sizeof(label), "%s%d", SUBRESULT_PFX, ++subresult_cnt);
if (boinc_resolve_filename(label, new_path, sizeof(new_path)))
return DC_ERR_INTERNAL;
/* We need the file name that will appear on the server */
p = strrchr(new_path, PATHSEP);
if (!p)
{
DC_log(LOG_ERR, "Failed to determine the on-server file name "
"of the subresult");
return DC_ERR_INTERNAL;
}
p++;
switch (mode)
{
case DC_FILE_REGULAR:
ret = _DC_copyFile(path, new_path);
if (ret)
return DC_ERR_SYSTEM;
break;
case DC_FILE_PERSISTENT:
#ifndef _WIN32
ret = link(path, new_path);
if (!ret)
break;
#endif
/* The client system may not support hard links so
* fall back to copying silently */
ret = _DC_copyFile(path, new_path);
if (ret)
return DC_ERR_SYSTEM;
break;
case DC_FILE_VOLATILE:
ret = rename(path, new_path);
if (!ret)
break;
/* If renaming fails, fall back to copying, but in this
* case we are also responsible for deleting the
* original */
ret = _DC_copyFile(path, new_path);
if (ret)
return DC_ERR_SYSTEM;
break;
case DC_FILE_REMOTE:
/* Ignore this case, entirely handled by BOINC */
break;
}
/* Stupid C++ */
std::string str = label;
ret = boinc_upload_file(str);
if (ret)
{
unlink(new_path);
return DC_ERR_INTERNAL;
}
DC_log(LOG_INFO, "File %s (%s) has been scheduled for upload",
logicalFileName, label);
snprintf(msg, sizeof(msg), "%s:%s:%s:%s", DCAPI_MSG_PFX, DC_MSG_UPLOAD,
p, logicalFileName);
DC_sendMessage(msg);
/* If we had to copy volatile files, delete the original only when
* we are sure the upload will happen */
if (mode == DC_FILE_VOLATILE)
unlink(path);
return 0;
}
int DC_initClient(void)
{
char path[PATH_MAX], *buf, label[32];
int i, ret;
FILE *f;
/* We leave the redirection to BOINC and only copy stdout.txt/stderr.txt
* to the final output location in DC_finishClient(). This means BOINC
* can rotate the files so they won't grow too big. */
if (boinc_init_diagnostics(BOINC_DIAG_REDIRECTSTDERR |
BOINC_DIAG_REDIRECTSTDOUT))
return DC_ERR_INTERNAL;
if (boinc_init())
return DC_ERR_INTERNAL;
/* Parse the config file if the master sent one */
buf = DC_resolveFileName(DC_FILE_IN, DC_CONFIG_FILE);
if (buf)
{
ret = _DC_parseCfg(buf);
if (ret && ret != DC_ERR_SYSTEM)
return ret;
}
free(buf);
/* Check if we are starting from a checkpoint file */
if ((f = boinc_fopen(LAST_CKPT_FILE, "r")))
{
fgets(path, sizeof(path), f);
fclose(f);
if (strlen(path))
last_complete_ckpt = strdup(path);
}
/* If the application did not generate a checkpoint file before, check
* if the master sent one */
else
last_complete_ckpt = DC_resolveFileName(DC_FILE_IN, CKPT_LABEL_IN);
if (last_complete_ckpt)
DC_log(LOG_INFO, "Found initial checkpoint file %s",
last_complete_ckpt);
/* Extract the WU name from init_data.xml */
if (boinc_is_standalone())
{
DC_log(LOG_NOTICE, "Running in stand-alone mode, some "
"functions are not available");
wu_name[0] = '\0';
}
else
{
APP_INIT_DATA init_data;
boinc_get_init_data(init_data);
strncpy(wu_name, init_data.wu_name, sizeof(wu_name));
}
/* Initialize all optional output files as empty to prevent
* <file_xfer_error>s */
for (i = 0; i < DC_getMaxSubresults(); i++)
{
snprintf(label, sizeof(label), "%s%d", SUBRESULT_PFX, i);
if (boinc_resolve_filename(label, path, sizeof(path)))
continue;
f = boinc_fopen(path, "w");
if (f)
fclose(f);
}
ret = boinc_resolve_filename(CKPT_LABEL_OUT, path, sizeof(path));
if (!ret)
{
f = boinc_fopen(path, "w");
if (f)
fclose(f);
}
DC_log(LOG_INFO, "DC-API initialized for work unit %s", wu_name);
return 0;
}
void boincrf_(const char* s, char* t, int s_len, int t_len) {
STRING_FROM_FORTRAN sff(s, s_len);
sff.strip_whitespace();
boinc_resolve_filename(sff.c_str(), t, t_len);
string_to_fortran(t, t_len);
}
void read_sequence_file(char *filename) {
FILE *sequence_file;
char current_line[200];
int current_length, line_length, name_length;
int i;
Sequence *current_sequence;
char c;
#ifdef _BOINC_
int retval;
char input_path[512];
retval = boinc_resolve_filename(filename, input_path, sizeof(input_path));
if (retval) {
fprintf(stderr, "ERROR, Could not resolve filename for reading sequences: [%s]\n", filename);
fprintf(stderr, "ERROR on line [%d], file [%s]\n", __LINE__, __FILE__);
exit(0);
}
sequence_file = boinc_fopen(input_path, "r");
#else
sequence_file = fopen(filename, "r");
#endif
if (sequence_file == NULL) {
fprintf(stderr, "ERROR, could not open filename to read sequence file: [%s]\n", filename);
fprintf(stderr, "ERROR on line [%d], file [%s]\n", __LINE__, __FILE__);
exit(0);
}
number_sequences = 0;
// fprintf(stderr, "mallocing sequences\n");
sequences = (Sequence**)malloc(sizeof(Sequence*));
// fprintf(stderr, "malloced sequences\n");
current_sequence = NULL;
current_length = 0;
while (NULL != fgets(current_line, 200, sequence_file)) {
if (strcmp(current_line, "") == 0 || strcmp(current_line, "\n") == 0) {
// fprintf(stdout, "skipping line: [%s]\n", current_line);
continue;
} else if (current_line[0] == '>') {
//start a new sequence
// fprintf(stdout, "starting new sequence with line: [%s]\n", current_line);
number_sequences++;
// fprintf(stderr, "reallocing sequences\n");
sequences = (Sequence**)realloc(sequences, number_sequences * sizeof(Sequence*));
// fprintf(stderr, "realloced sequences\n");
sequences[number_sequences - 1] = (Sequence*)malloc(sizeof(Sequence));
current_sequence = sequences[number_sequences - 1];
name_length = strlen(current_line) - 1;
current_sequence->name = (char*)malloc(sizeof(char) * (name_length));
for (i = 1; i < name_length; i++) current_sequence->name[i-1] = current_line[i];
current_sequence->name[name_length-1] = '\0';
current_sequence->nucleotides = NULL;
current_length = 0;
// fprintf(stdout, "reading new sequence, named: [%s]\n", current_sequence->name);
} else {
//append the current line to the sequence
// fprintf(stdout, "appending line to sequence: [%s]\n", current_line);
line_length = strlen(current_line);
// printf("current line is [%s], length [%d]\n", current_line, line_length);
for (i = 0; i < line_length; i++) {
c = toupper(current_line[i]);
if (c != 'A' && c != 'C' && c != 'G' && c != 'T' && c != 'X') {
current_line[i] = '\0';
line_length = i;
break;
}
}
// printf("current line is [%s], length [%d]\n", current_line, line_length);
// current_line[line_length] = '\0';
if (current_length == 0) {
// fprintf(stderr, "mallocing nucleotides\n");
current_sequence->nucleotides = (char*)malloc(line_length + 1);
// fprintf(stderr, "malloced nucleotides\n");
} else {
// fprintf(stderr, "reallocing nucleotides\n");
current_sequence->nucleotides = (char*)realloc(current_sequence->nucleotides, current_length + line_length + 1);
// fprintf(stderr, "realloced nucleotides\n");
}
for (i = 0; i < line_length; i++) current_sequence->nucleotides[current_length + i] = current_line[i];
current_sequence->nucleotides[current_length + line_length] = '\0';
current_length += line_length;
current_sequence->length = current_length;
for (i = 0; i < current_sequence->length; i++) {
c = toupper(current_sequence->nucleotides[i]);
if (c != 'A' && c != 'C' && c != 'G' && c != 'T' && c != 'X') {
printf("error in sequence, character at [%d] is not ACGTX: [%c][%d]\n", i, c, (int)c);
exit(0);
}
}
// printf("nucleotides is now [%s], length [%d]\n\n", current_sequence->nucleotides, current_sequence->length);
}
}
fclose(sequence_file);
// printf("read %d sequences\n", number_sequences);
// for (i = 0; i < number_sequences; i++) {
// printf("[%s]\n", sequences[i]->name);
// printf("[%d] %s\n", sequences[i]->length, sequences[i]->nucleotides);
// }
/**
* Convert the sequences to uppercase to make things easier (so we don't have to check for lowercase as well).
*/
sequences_to_uppercase();
/**
* Calculate the background probabilities since we only need to do this once.
*/
calculate_background_nucleotide_probabilities();
/**
* Testing: print out the sequences
*/
/*
for (i = 0; i < number_sequences; i++) {
current_sequence = sequences[i];
printf("name: [%s]\n", current_sequence->name);
printf("nucleotides: [%s]\n", current_sequence->nucleotides);
printf("length: [%d]\n", current_sequence->length);
printf("strlen(nucleotides): [%d]\n", (int)strlen(current_sequence->nucleotides));
printf("background_probability[A]: %.15lf\n", current_sequence->background_probability[A_POSITION]);
printf("background_probability[C]: %.15lf\n", current_sequence->background_probability[C_POSITION]);
printf("background_probability[G]: %.15lf\n", current_sequence->background_probability[G_POSITION]);
printf("background_probability[T]: %.15lf\n", current_sequence->background_probability[T_POSITION]);
if (strlen(current_sequence->nucleotides) != current_sequence->length) {
//sanity check
fprintf(stderr, "ERROR! strlen(nucleotides) != length!\n");
exit(0);
}
printf("\n");
}
*/
}
int VBOX_JOB::parse() {
MIOFILE mf;
std::string str;
char buf[1024];
boinc_resolve_filename(JOB_FILENAME, buf, sizeof(buf));
FILE* f = boinc_fopen(buf, "r");
if (!f) {
vboxlog_msg("VBOX_JOB::parse(): can't open job file %s", buf);
return ERR_FOPEN;
}
mf.init_file(f);
XML_PARSER xp(&mf);
if (!xp.parse_start("vbox_job")) return ERR_XML_PARSE;
while (!xp.get_tag()) {
if (!xp.is_tag) {
vboxlog_msg("VBOX_JOB::parse(): unexpected text %s", xp.parsed_tag);
continue;
}
if (xp.match_tag("/vbox_job")) {
fclose(f);
return 0;
}
else if (xp.parse_string("vm_disk_controller_type", vm_disk_controller_type)) continue;
else if (xp.parse_string("vm_disk_controller_model", vm_disk_controller_model)) continue;
else if (xp.parse_string("os_name", os_name)) continue;
else if (xp.parse_double("memory_size_mb", memory_size_mb)) continue;
else if (xp.parse_double("job_duration", job_duration)) continue;
else if (xp.parse_double("minimum_checkpoint_interval", minimum_checkpoint_interval)) continue;
else if (xp.parse_double("minimum_heartbeat_interval", minimum_heartbeat_interval)) continue;
else if (xp.parse_string("fraction_done_filename", fraction_done_filename)) continue;
else if (xp.parse_string("heartbeat_filename", heartbeat_filename)) continue;
else if (xp.parse_string("completion_trigger_file", completion_trigger_file)) continue;
else if (xp.parse_string("temporary_exit_trigger_file", temporary_exit_trigger_file)) continue;
else if (xp.parse_bool("enable_cern_dataformat", enable_cern_dataformat)) continue;
else if (xp.parse_bool("enable_network", enable_network)) continue;
else if (xp.parse_bool("network_bridged_mode", network_bridged_mode)) continue;
else if (xp.parse_bool("enable_shared_directory", enable_shared_directory)) continue;
else if (xp.parse_bool("enable_scratch_directory", enable_scratch_directory)) continue;
else if (xp.parse_bool("enable_floppyio", enable_floppyio)) continue;
else if (xp.parse_bool("enable_cache_disk", enable_cache_disk)) continue;
else if (xp.parse_bool("enable_isocontextualization", enable_isocontextualization)) continue;
else if (xp.parse_bool("enable_remotedesktop", enable_remotedesktop)) continue;
else if (xp.parse_bool("enable_gbac", enable_gbac)) continue;
else if (xp.parse_bool("enable_screenshots_on_error", enable_screenshots_on_error)) continue;
else if (xp.parse_bool("enable_graphics_support", enable_graphics_support)) continue;
else if (xp.parse_bool("enable_vm_savestate_usage", enable_vm_savestate_usage)) continue;
else if (xp.parse_bool("disable_automatic_checkpoints", disable_automatic_checkpoints)) continue;
else if (xp.parse_bool("boot_iso", boot_iso)) continue;
else if (xp.parse_int("pf_guest_port", pf_guest_port)) continue;
else if (xp.parse_int("pf_host_port", pf_host_port)) continue;
else if (xp.parse_string("copy_to_shared", str)) {
copy_to_shared.push_back(str);
continue;
}
else if (xp.parse_string("trickle_trigger_file", str)) {
trickle_trigger_files.push_back(str);
continue;
}
else if (xp.parse_string("intermediate_upload_file", str)) {
VBOX_INTERMEDIATE_UPLOAD iu;
iu.clear();
iu.file = str;
intermediate_upload_files.push_back(iu);
continue;
}
else if (xp.match_tag("port_forward")) {
VBOX_PORT_FORWARD pf;
pf.clear();
pf.parse(xp);
if (pf.nports) {
VBOX_PORT_FORWARD pf_range;
pf_range = pf;
pf_range.nports = 0;
for (int i = 0; i < pf.nports; ++i) {
port_forwards.push_back(pf_range);
pf_range.host_port++;
pf_range.guest_port++;
}
} else {
port_forwards.push_back(pf);
}
}
vboxlog_msg("VBOX_JOB::parse(): unexpected text %s", xp.parsed_tag);
}
fclose(f);
return ERR_XML_PARSE;
}
