I am trying to create kernel argument for a structure,but after executing clSetKernelArg line,program exit the system.
predict_component=(component *)malloc(sizeof(component)*component_count);
predict_component_mem=clCreateBuffer(al_context,CL_MEM_READ_WRITE | CL_MEM_COPY_HOST_PTR,sizeof(component)*component_count,predict_component,&al_status);
al_status = clSetKernelArg(al_kernel[0], 0, sizeof(cl_mem), (void *)&predict_component_mem);
**component is a basic structure.
I am totally unable to locate the cause,any help will be much appreciated.
Related
I work with a Mac. I have been trying to make a multiple sequence alignment in Python using Muscle. This is the code I have been running:
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(input="testunaligned.fasta", out="testunaligned.aln", clwstrict=True)
print(cline)
from Bio import AlignIO
align = AlignIO.read(open("testunaligned.aln"), "clustal")
print(align)
I keep getting the following error:
FileNotFoundError: [Errno 2] No such file or directory: 'testunaligned.aln'
Does anyone know how I could fix this? I am very new to Python and computer science in general, and I am totally at a loss. Thanks!
cline in your code is an instance of MuscleCommandline object that you initialized with all the parameters. After the initialization, this instance can run muscle, but it will only do that if you call it. That means you have to invoke cline()
When you simply print the cline object, it will return a string that corresponds to the command you can manually run on the command line to get the same result as when you invoke cline().
And here the working code:
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(
input="testunaligned.fasta",
out="testunaligned.aln",
clwstrict=True
)
print(cline)
cline() # this is where mucle runs
from Bio import AlignIO
align = AlignIO.read(open("testunaligned.aln"), "clustal")
print(align)
I am trying to put together and example of coding inline assembly code in a 'C' program. I have not had any success. I am using GCC 4.9.0. As near as I can tell my syntax is correct. However the build blows up with the following errors:
/tmp/ccqC2wtq.s:48: Error: syntax error; found `(', expected `,'
Makefile:51: recipe for target 'all' failed
/tmp/ccqC2wtq.s:48: Error: junk at end of line: `(31)'
/tmp/ccqC2wtq.s:49: Error: syntax error; found `(', expected `,'
/tmp/ccqC2wtq.s:49: Error: junk at end of line: `(9)'
These are related to the input/output/clobbers lines in the code. Anyone have an idea where I went wrong?
asm volatile("li 7, %0\n" // load destination address
"li 8, %1\n" // load source address
"li 9, 100\n" // load count
// save source address for return
"mr 3,7\n"
// prepare for loop
"subi 8,8,1\n"
"subi 9,9,1\n"
// perform copy
"1:\n"
"lbzu 10,2(8)\n"
"stbu 10,2(7)\n"
"subi 9,9,1\n" // Decrement the count
"bne 1b\n" // If zero, we've finished
"blr\n"
: // no outputs
: "m" (array), "m" (stringArray)
: "r7", "r8"
);
It's not clear what you are trying to do with the initial instructions:
li 7, %0
li 8, %1
Do you want to load the address of the variables into those registers? In general, this is not possible because the address is not representable in an immediate operand. The easiest way out is to avoid using r7 and r8, and instead use %0 and %1 directly as the register names. It seems that you want to use these registers as base addresses, so you should use the b constraint:
: "b" (array), "b" (stringArray)
Then GCC will take care of the details of materializing the address in a suitable fashion.
You cannot return using blr from inline assembler because it's not possible to tear down the stack frame GCC created. You also need to double-check the clobbers and make sure that you list all the things you clobber (including condition codes, memory, and overwritten input operands).
I was able to get this working by declaring a pair of pointers and initializing them with the addresses of the arrays. I didn't realize that the addresses wouldn't be available directly. I've used inline assembly very sparsely in the past, usually just
to raise or lower interrupt masks, not to do anything that references variables. I just
had some folks who wanted an example. And the "blr" was leftover when I copied a
snipet of a pure assembly routine to use as a starting point. Thanks for the responses.
The final code piece looks like this:
int main()
{
char * stringArrayPtr;
unsigned char * myArrayPtr;
unsigned char myArray[100];
stringArrayPtr = (char *)&stringArray;
myArrayPtr = myArray;
asm volatile(
"lwz 7,%[myArrayPtr]\n" // load destination address
"lwz 8, %[stringArrayPtr]\n" // load source address
"li 9, 100\n" // load count
"mr 3,7\n" // save source address for return
"subi 8,8,1\n" // prepare for loop
"subi 9,9,1\n"
"1:\n" // perform copy
"lbzu 10,1(8)\n"
"stbu 10,1(7)\n"
"subic. 9,9,1\n" // Decrement the count
"bne 1b\n" // If zero, we've finished
// The outputs / inputs / clobbered list
// No output variables are specified here
// See GCC documentation on extended assembly for details.
:
: [stringArrayPtr] "m" (stringArrayPtr), [myArrayPtr]"m"(myArrayPtr)
: "7","8","9","10"
);
}
I have a korn shell script which will pass 4 parameters to a Pro*C file
The syntax of the korn shell script are below:
### $command_dir/proc_file_name / $deptid $txdate $pid
### I hardcode the values for testing
$command_dir/proc_file_name / 701 20170109 201701094444001
The syntax of the Pro*C file:
....
main(argc, argv)
int argc
char *argv[];
username.len=strlen(argv[1]);
strncpy((char*)username.arr, argv[1],username.len);
username.arr[username.len]='\0';
deptid.len=strlen(argv[1]);
strncpy((char*)deptid.arr, argv[1],deptid.len);
deptid.arr[deptid.len]='\0';
txdate.len=strlen(argv[1]);
strncpy((char*)txdate.arr, argv[1],txdate.len);
txdate.arr[txdate.len]='\0';
pid=atoi(argv[4]);
printf("\n%s\n", username);
printf("\n%d\n", deptid);
printf("\n%d\n", txdate);
printf("\n%d\n", pid);
....
I found that the values of the parameters were not I put.
Please help...
Many Many thanks
You are using the same array index of 1 for username, deptid, and txdate. Correct that and you would be good.
Accessing argv[1] etc., without checking argc isn't a good practice. When invoked without arguments, your code will result in a core dump.
Also, I don't think your code has the right syntax. Can you please paste the code that compiles?
I was trying to debug a Python 2 script running on Raspbian (Raspberry Pi flavoured Debian Linux) which had code like
euid = os.geteuid()
if euid != 0:
print("you must be root!")
exit(1)
It seemed like, in the user's environment, euid would sometimes be nonzero even if the script was called with sudo.
To investigate whether this was actually the case, I tried to figure out what os.geteuid() is actually doing.
Since the os module is pretty OS-specific by its nature, the source doesn't actually have a clear definition for os.geteuid().
I also tried hg cloneing the source and compiling it, then using inspect.findsource(os.geteuid), but:
TypeError: <built-in function geteuid> is not a module, class, method, function, traceback, frame, or code object
It's... a builtin? Then "geteuid" in dir(__import__("__builtin__")) should be True, but it isn't.
Is geteuid's definition hidden because it could be spoofed into returning the wrong thing (and that would be bad)? Where can I see these sorts of functions' actual source?
ASCII stupid question, get a stupid ANSI.
I did try full-text searching the source, but apparently I used the wrong command the first time and gave up.
$ grep -rnw '.' -e "geteuid"
./Misc/setuid-prog.c:129: uid_t euid = geteuid();
./Lib/site.py:209: if hasattr(os, "getuid") and hasattr(os, "geteuid"):
./Lib/site.py:211: if os.geteuid() != os.getuid():
./Lib/test/test_shutil.py:84: #unittest.skipIf(hasattr(os, 'geteuid') and os.geteuid() == 0,
./Lib/test/test_httpservers.py:339: if os.name == 'posix' and os.geteuid() != 0:
./Lib/test/test_httpservers.py:395:#unittest.skipIf(hasattr(os, 'geteuid') and os.geteuid() == 0,
./Lib/test/test_spwd.py:8:#unittest.skipUnless(hasattr(os, 'geteuid') and os.geteuid() == 0,
./Lib/test/test_posix.py:44: "getegid", "geteuid", "getgid", "getgroups",
./Lib/test/test_argparse.py:1532:#unittest.skipIf(hasattr(os, 'geteuid') and os.geteuid() == 0,
Binary file ./Lib/tarfile.py matches
./Lib/rexec.py:148: 'getcwd', 'getuid', 'getgid', 'geteuid', 'getegid')
Binary file ./Modules/posixmodule.o matches
./Modules/posixmodule.c:4047:"geteuid() -> euid\n\n\
./Modules/posixmodule.c:4053: return _PyInt_FromUid(geteuid());
./Modules/posixmodule.c:8944: {"geteuid", posix_geteuid, METH_NOARGS, posix_geteuid__doc__},
./Doc/library/rexec.rst:234: 'times', 'uname', 'getpid', 'getppid', 'getcwd', 'getuid', 'getgid', 'geteuid',
./Doc/library/os.rst:136:.. function:: geteuid()
Binary file ./python matches
Binary file ./libpython2.7.a matches
./Modules/posixmodule.c:4053, indeed:
#ifdef HAVE_GETEUID
PyDoc_STRVAR(posix_geteuid__doc__,
"geteuid() -> euid\n\n\
Return the current process's effective user id.");
static PyObject *
posix_geteuid(PyObject *self, PyObject *noargs)
{
return _PyInt_FromUid(geteuid());
}
#endif
I don't know what I expected, subprocess.check_output(["id"])?
It uses the C standard library, it's never wrong.
I am trying to call cudppSort to sort a set of keys/values. I'm using the following code to set up the sort algorithm:
CUDPPConfiguration config;
config.op = CUDPP_ADD;
config.datatype = CUDPP_UINT;
config.algorithm = CUDPP_SORT_RADIX;
config.options = CUDPP_OPTION_KEY_VALUE_PAIRS | CUDPP_OPTION_FORWARD | CUDPP_OPTION_EXCLUSIVE;
CUDPPHandle planHandle;
CUDPPResult result = cudppPlan(&planHandle, config, number_points, 1, 0);
if (CUDPP_SUCCESS != result) {
printf("ERROR creating CUDPPPlan\n");
exit(-1);
}
The program exits, however on the line:
CUDPPResult result = cudppPlan(&planHandle, config, number_points, 1, 0);
and prints to stdout:
Cuda error: allocScanStorage in file 'c:/the/path/to/release1.1/cudpp/src/app/scan_app.cu' in line 279 : invalid configuration argument.
I looked at the line in scan_app.cu. It is,
CUT_CHECK_ERROR("allocScanStorage");
So apparently my configuration has an error that is causing the allocScanStorage to bomb out. There are only two calls to CUDA_SAFE_CALL in the function and I don't see a reason why either has anything to do with the configuration.
What is wrong with my configuration?
So that this doesn't sit around as an unanswered question (I'm not sure if this is the right SO etiquette but it seems like an answered question shouldn't sit around unanswered...), I'm copying the comment I made above here as an answer since it was the solution:
I figured this out (I'm still learning CUDA at the moment.) Because the error checking is asynchronous errors can show up in strange places if you don't check for them from time to time. My code had caused an error before I called cudppPlan but because I didn't check for errors the cudppPlan reported the error as if it was in cudppPlan.