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Commit 5c20d591 authored by Lukáš Krupčík's avatar Lukáš Krupčík
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docs.it4i/anselm-cluster-documentation/software/intel-xeon-phi.md
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− 165
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......@@ -19,7 +19,7 @@ To set up the environment module "Intel" has to be loaded
$ module load intel/13.5.192
```
Information about the hardware can be obtained by running the micinfo program on the host.
Information about the hardware can be obtained by running the micinfo program on the host.
```bash
$ /usr/bin/micinfo
......@@ -32,61 +32,61 @@ The output of the "micinfo" utility executed on one of the Anselm node is as fol
Created Mon Jul 22 00:23:50 2013
System Info
HOST OS : Linux
OS Version : 2.6.32-279.5.2.bl6.Bull.33.x86_64
Driver Version : 6720-15
MPSS Version : 2.1.6720-15
Host Physical Memory : 98843 MB
System Info
HOST OS : Linux
OS Version : 2.6.32-279.5.2.bl6.Bull.33.x86_64
Driver Version : 6720-15
MPSS Version : 2.1.6720-15
Host Physical Memory : 98843 MB
Device No: 0, Device Name: mic0
Version
Flash Version : 2.1.03.0386
SMC Firmware Version : 1.15.4830
SMC Boot Loader Version : 1.8.4326
uOS Version : 2.6.38.8-g2593b11
Device Serial Number : ADKC30102482
Board
Vendor ID : 0x8086
Device ID : 0x2250
Subsystem ID : 0x2500
Coprocessor Stepping ID : 3
PCIe Width : x16
PCIe Speed : 5 GT/s
PCIe Max payload size : 256 bytes
PCIe Max read req size : 512 bytes
Coprocessor Model : 0x01
Coprocessor Model Ext : 0x00
Coprocessor Type : 0x00
Coprocessor Family : 0x0b
Coprocessor Family Ext : 0x00
Coprocessor Stepping : B1
Board SKU : B1PRQ-5110P/5120D
ECC Mode : Enabled
SMC HW Revision : Product 225W Passive CS
Cores
Total No of Active Cores : 60
Voltage : 1032000 uV
Frequency : 1052631 kHz
Thermal
Fan Speed Control : N/A
Fan RPM : N/A
Fan PWM : N/A
Die Temp : 49 C
GDDR
GDDR Vendor : Elpida
GDDR Version : 0x1
GDDR Density : 2048 Mb
GDDR Size : 7936 MB
GDDR Technology : GDDR5
GDDR Speed : 5.000000 GT/s
GDDR Frequency : 2500000 kHz
GDDR Voltage : 1501000 uV
Version
Flash Version : 2.1.03.0386
SMC Firmware Version : 1.15.4830
SMC Boot Loader Version : 1.8.4326
uOS Version : 2.6.38.8-g2593b11
Device Serial Number : ADKC30102482
Board
Vendor ID : 0x8086
Device ID : 0x2250
Subsystem ID : 0x2500
Coprocessor Stepping ID : 3
PCIe Width : x16
PCIe Speed : 5 GT/s
PCIe Max payload size : 256 bytes
PCIe Max read req size : 512 bytes
Coprocessor Model : 0x01
Coprocessor Model Ext : 0x00
Coprocessor Type : 0x00
Coprocessor Family : 0x0b
Coprocessor Family Ext : 0x00
Coprocessor Stepping : B1
Board SKU : B1PRQ-5110P/5120D
ECC Mode : Enabled
SMC HW Revision : Product 225W Passive CS
Cores
Total No of Active Cores : 60
Voltage : 1032000 uV
Frequency : 1052631 kHz
Thermal
Fan Speed Control : N/A
Fan RPM : N/A
Fan PWM : N/A
Die Temp : 49 C
GDDR
GDDR Vendor : Elpida
GDDR Version : 0x1
GDDR Density : 2048 Mb
GDDR Size : 7936 MB
GDDR Technology : GDDR5
GDDR Speed : 5.000000 GT/s
GDDR Frequency : 2500000 kHz
GDDR Voltage : 1501000 uV
```
Offload Mode
......@@ -113,16 +113,16 @@ A very basic example of code that employs offload programming technique is shown
int main(int argc, char* argv[])
{
const int niter = 100000;
double result = 0;
#pragma offload target(mic)
for (int i = 0; i < niter; ++i) {
const double t = (i + 0.5) / niter;
result += 4.0 / (t * t + 1.0);
}
result /= niter;
std::cout << "Pi ~ " << result << 'n';
const int niter = 100000;
double result = 0;
#pragma offload target(mic)
for (int i = 0; i < niter; ++i) {
const double t = (i + 0.5) / niter;
result += 4.0 / (t * t + 1.0);
}
result /= niter;
std::cout << "Pi ~ " << result << 'n';
}
```
......@@ -159,63 +159,63 @@ One way of paralelization a code for Xeon Phi is using OpenMP directives. The fo
// MIC function to add two vectors
__attribute__((target(mic))) add_mic(T *a, T *b, T *c, int size) {
int i = 0;
#pragma omp parallel for
for (i = 0; i < size; i++)
c[i] = a[i] + b[i];
int i = 0;
#pragma omp parallel for
for (i = 0; i < size; i++)
c[i] = a[i] + b[i];
}
// CPU function to add two vectors
void add_cpu (T *a, T *b, T *c, int size) {
int i;
for (i = 0; i < size; i++)
c[i] = a[i] + b[i];
int i;
for (i = 0; i < size; i++)
c[i] = a[i] + b[i];
}
// CPU function to generate a vector of random numbers
void random_T (T *a, int size) {
int i;
for (i = 0; i < size; i++)
a[i] = rand() % 10000; // random number between 0 and 9999
int i;
for (i = 0; i < size; i++)
a[i] = rand() % 10000; // random number between 0 and 9999
}
// CPU function to compare two vectors
int compare(T *a, T *b, T size ){
int pass = 0;
int i;
for (i = 0; i < size; i++){
if (a[i] != b[i]) {
printf("Value mismatch at location %d, values %d and %dn",i, a[i], b[i]);
pass = 1;
}
}
if (pass == 0) printf ("Test passedn"); else printf ("Test Failedn");
return pass;
int pass = 0;
int i;
for (i = 0; i < size; i++){
if (a[i] != b[i]) {
printf("Value mismatch at location %d, values %d and %dn",i, a[i], b[i]);
pass = 1;
}
}
if (pass == 0) printf ("Test passedn"); else printf ("Test Failedn");
return pass;
}
int main()
{
int i;
random_T(in1, SIZE);
random_T(in2, SIZE);
int i;
random_T(in1, SIZE);
random_T(in2, SIZE);
#pragma offload target(mic) in(in1,in2) inout(res)
{
#pragma offload target(mic) in(in1,in2) inout(res)
{
// Parallel loop from main function
#pragma omp parallel for
for (i=0; i<SIZE; i++)
res[i] = in1[i] + in2[i];
// Parallel loop from main function
#pragma omp parallel for
for (i=0; i<SIZE; i++)
res[i] = in1[i] + in2[i];
// or parallel loop is called inside the function
add_mic(in1, in2, res, SIZE);
// or parallel loop is called inside the function
add_mic(in1, in2, res, SIZE);
}
}
//Check the results with CPU implementation
T res_cpu[SIZE];
add_cpu(in1, in2, res_cpu, SIZE);
compare(res, res_cpu, SIZE);
//Check the results with CPU implementation
T res_cpu[SIZE];
add_cpu(in1, in2, res_cpu, SIZE);
compare(res, res_cpu, SIZE);
}
```
......@@ -282,48 +282,48 @@ Following example show how to automatically offload an SGEMM (single precision -
int main(int argc, char **argv)
{
float *A, *B, *C; /* Matrices */
float *A, *B, *C; /* Matrices */
MKL_INT N = 2560; /* Matrix dimensions */
MKL_INT LD = N; /* Leading dimension */
int matrix_bytes; /* Matrix size in bytes */
int matrix_elements; /* Matrix size in elements */
MKL_INT N = 2560; /* Matrix dimensions */
MKL_INT LD = N; /* Leading dimension */
int matrix_bytes; /* Matrix size in bytes */
int matrix_elements; /* Matrix size in elements */
float alpha = 1.0, beta = 1.0; /* Scaling factors */
char transa = 'N', transb = 'N'; /* Transposition options */
float alpha = 1.0, beta = 1.0; /* Scaling factors */
char transa = 'N', transb = 'N'; /* Transposition options */
int i, j; /* Counters */
int i, j; /* Counters */
matrix_elements = N * N;
matrix_bytes = sizeof(float) * matrix_elements;
matrix_elements = N * N;
matrix_bytes = sizeof(float) * matrix_elements;
/* Allocate the matrices */
A = malloc(matrix_bytes); B = malloc(matrix_bytes); C = malloc(matrix_bytes);
/* Allocate the matrices */
A = malloc(matrix_bytes); B = malloc(matrix_bytes); C = malloc(matrix_bytes);
/* Initialize the matrices */
for (i = 0; i < matrix_elements; i++) {
A[i] = 1.0; B[i] = 2.0; C[i] = 0.0;
}
/* Initialize the matrices */
for (i = 0; i < matrix_elements; i++) {
A[i] = 1.0; B[i] = 2.0; C[i] = 0.0;
}
printf("Computing SGEMM on the hostn");
sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);
printf("Computing SGEMM on the hostn");
sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);
printf("Enabling Automatic Offloadn");
/* Alternatively, set environment variable MKL_MIC_ENABLE=1 */
mkl_mic_enable();
printf("Enabling Automatic Offloadn");
/* Alternatively, set environment variable MKL_MIC_ENABLE=1 */
mkl_mic_enable();
int ndevices = mkl_mic_get_device_count(); /* Number of MIC devices */
printf("Automatic Offload enabled: %d MIC devices presentn", ndevices);
int ndevices = mkl_mic_get_device_count(); /* Number of MIC devices */
printf("Automatic Offload enabled: %d MIC devices presentn", ndevices);
printf("Computing SGEMM with automatic workdivisionn");
sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);
printf("Computing SGEMM with automatic workdivisionn");
sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);
/* Free the matrix memory */
free(A); free(B); free(C);
/* Free the matrix memory */
free(A); free(B); free(C);
printf("Donen");
printf("Donen");
return 0;
return 0;
}
```
......@@ -349,10 +349,10 @@ The output of a code should look similar to following listing, where lines start
Enabling Automatic Offload
Automatic Offload enabled: 1 MIC devices present
Computing SGEMM with automatic workdivision
[MKL] [MIC --] [AO Function] SGEMM
[MKL] [MIC --] [AO SGEMM Workdivision] 0.00 1.00
[MKL] [MIC 00] [AO SGEMM CPU Time] 0.463351 seconds
[MKL] [MIC 00] [AO SGEMM MIC Time] 0.179608 seconds
[MKL] [MIC --] [AO Function] SGEMM
[MKL] [MIC --] [AO SGEMM Workdivision] 0.00 1.00
[MKL] [MIC 00] [AO SGEMM CPU Time] 0.463351 seconds
[MKL] [MIC 00] [AO SGEMM MIC Time] 0.179608 seconds
[MKL] [MIC 00] [AO SGEMM CPU->MIC Data] 52428800 bytes
[MKL] [MIC 00] [AO SGEMM MIC->CPU Data] 26214400 bytes
Done
......@@ -479,23 +479,23 @@ After executing the complied binary file, following output should be displayed.
Number of available platforms: 1
Platform names:
[0] Intel(R) OpenCL [Selected]
[0] Intel(R) OpenCL [Selected]
Number of devices available for each type:
CL_DEVICE_TYPE_CPU: 1
CL_DEVICE_TYPE_GPU: 0
CL_DEVICE_TYPE_ACCELERATOR: 1
CL_DEVICE_TYPE_CPU: 1
CL_DEVICE_TYPE_GPU: 0
CL_DEVICE_TYPE_ACCELERATOR: 1
** Detailed information for each device ***
CL_DEVICE_TYPE_CPU[0]
CL_DEVICE_NAME: Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
CL_DEVICE_AVAILABLE: 1
CL_DEVICE_NAME: Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
CL_DEVICE_AVAILABLE: 1
...
CL_DEVICE_TYPE_ACCELERATOR[0]
CL_DEVICE_NAME: Intel(R) Many Integrated Core Acceleration Card
CL_DEVICE_AVAILABLE: 1
CL_DEVICE_NAME: Intel(R) Many Integrated Core Acceleration Card
CL_DEVICE_AVAILABLE: 1
...
```
......@@ -579,23 +579,23 @@ An example of basic MPI version of "hello-world" example in C language, that can
#include <mpi.h>
int main (argc, argv)
int argc;
char *argv[];
int argc;
char *argv[];
{
int rank, size;
int rank, size;
int len;
char node[MPI_MAX_PROCESSOR_NAME];
int len;
char node[MPI_MAX_PROCESSOR_NAME];
MPI_Init (&argc, &argv); /* starts MPI */
MPI_Comm_rank (MPI_COMM_WORLD, &rank); /* get current process id */
MPI_Comm_size (MPI_COMM_WORLD, &size); /* get number of processes */
MPI_Init (&argc, &argv); /* starts MPI */
MPI_Comm_rank (MPI_COMM_WORLD, &rank); /* get current process id */
MPI_Comm_size (MPI_COMM_WORLD, &size); /* get number of processes */
MPI_Get_processor_name(node,&len);
MPI_Get_processor_name(node,&len);
printf( "Hello world from process %d of %d on host %s n", rank, size, node );
MPI_Finalize();
return 0;
printf( "Hello world from process %d of %d on host %s n", rank, size, node );
MPI_Finalize();
return 0;
}
```
......@@ -722,8 +722,8 @@ The output should be again similar to:
Please note that the **"mpiexec.hydra"** requires a file the MIC filesystem. If the file is missing please contact the system administrators. A simple test to see if the file is present is to execute:
```bash
$ ssh mic0 ls /bin/pmi_proxy
/bin/pmi_proxy
$ ssh mic0 ls /bin/pmi_proxy
/bin/pmi_proxy
```
**Execution on host - MPI processes distributed over multiple accelerators on multiple nodes**
......@@ -769,8 +769,8 @@ The launch the MPI program use:
```bash
$ mpiexec.hydra -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-genv I_MPI_FABRICS_LIST tcp
-genv I_MPI_FABRICS shm:tcp
-genv I_MPI_TCP_NETMASK=10.1.0.0/16
-genv I_MPI_FABRICS shm:tcp
-genv I_MPI_TCP_NETMASK=10.1.0.0/16
-host cn204-mic0 -n 4 ~/mpi-test-mic
: -host cn205-mic0 -n 6 ~/mpi-test-mic
```
......@@ -779,8 +779,8 @@ or using mpirun:
```bash
$ mpirun -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-genv I_MPI_FABRICS_LIST tcp
-genv I_MPI_FABRICS shm:tcp
-genv I_MPI_TCP_NETMASK=10.1.0.0/16
-genv I_MPI_FABRICS shm:tcp
-genv I_MPI_TCP_NETMASK=10.1.0.0/16
-host cn204-mic0 -n 4 ~/mpi-test-mic
: -host cn205-mic0 -n 6 ~/mpi-test-mic
```
......@@ -805,8 +805,8 @@ The same way MPI program can be executed on multiple hosts:
```bash
$ mpiexec.hydra -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-genv I_MPI_FABRICS_LIST tcp
-genv I_MPI_FABRICS shm:tcp
-genv I_MPI_TCP_NETMASK=10.1.0.0/16
-genv I_MPI_FABRICS shm:tcp
-genv I_MPI_TCP_NETMASK=10.1.0.0/16
-host cn204 -n 4 ~/mpi-test
: -host cn205 -n 6 ~/mpi-test
```
......@@ -822,7 +822,7 @@ In the previous section we have compiled two binary files, one for hosts "**mpi-
$ mpiexec.hydra
-genv I_MPI_FABRICS_LIST tcp
-genv I_MPI_FABRICS shm:tcp
-genv I_MPI_TCP_NETMASK=10.1.0.0/16
-genv I_MPI_TCP_NETMASK=10.1.0.0/16
-genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-host cn205 -n 2 ~/mpi-test
: -host cn205-mic0 -n 2 ~/mpi-test-mic
......@@ -851,7 +851,7 @@ An example of a machine file that uses 2 >hosts (**cn205** and **cn206**) and 2
cn206-mic0:2
```
In addition if a naming convention is set in a way that the name of the binary for host is **"bin_name"** and the name of the binary for the accelerator is **"bin_name-mic"** then by setting up the environment variable **I_MPI_MIC_POSTFIX** to **"-mic"** user do not have to specify the names of booth binaries. In this case mpirun needs just the name of the host binary file (i.e. "mpi-test") and uses the suffix to get a name of the binary for accelerator (i..e. "mpi-test-mic").
In addition if a naming convention is set in a way that the name of the binary for host is **"bin_name"** and the name of the binary for the accelerator is **"bin_name-mic"** then by setting up the environment variable **I_MPI_MIC_POSTFIX** to **"-mic"** user do not have to specify the names of booth binaries. In this case mpirun needs just the name of the host binary file (i.e. "mpi-test") and uses the suffix to get a name of the binary for accelerator (i..e. "mpi-test-mic").
```bash
$ export I_MPI_MIC_POSTFIX=-mic
......@@ -864,8 +864,8 @@ To run the MPI code using mpirun and the machine file "hosts_file_mix" use:
-genv I_MPI_FABRICS shm:tcp
-genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-genv I_MPI_FABRICS_LIST tcp
-genv I_MPI_FABRICS shm:tcp
-genv I_MPI_TCP_NETMASK=10.1.0.0/16
-genv I_MPI_FABRICS shm:tcp
-genv I_MPI_TCP_NETMASK=10.1.0.0/16
-machinefile hosts_file_mix
~/mpi-test
```
......@@ -901,4 +901,4 @@ Please note each host or accelerator is listed only per files. User has to speci
Optimization
------------
For more details about optimization techniques please read Intel document [Optimization and Performance Tuning for Intel® Xeon Phi™ Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization")
For more details about optimization techniques please read Intel document [Optimization and Performance Tuning for Intel® Xeon Phi™ Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization")
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