Changes between Initial Version and Version 1 of mpich/2008-07-20_YM_MPI_Course

Timestamp:

Jul 20, 2008, 5:35:00 PM (16 years ago)

Author:

jazz

Comment:

--

mpich/2008-07-20_YM_MPI_Course

@@ +1 @@
+ * 使用你的帳號登入: ym**
+{{{
+login as: ym000
+ym000@140.129.162.12's password: ******
+ym000@bio001:~$ ssh-keygen -t rsa
+}}}
+ * 產生 SSH 認證金鑰
+{{{
+Generating public/private rsa key pair.
+Enter file in which to save the key (/home/ym000/.ssh/id_rsa):
+Created directory '/home/ym000/.ssh'.
+Enter passphrase (empty for no passphrase):
+Enter same passphrase again:
+Your identification has been saved in /home/ym000/.ssh/id_rsa.
+Your public key has been saved in /home/ym000/.ssh/id_rsa.pub.
+The key fingerprint is:
+2a:6c:05:f8:24:38:db:79:b9:4f:0c:74:da:c5:16:05 ym000@bio001
+}}}
+ * 進行金鑰交換
+{{{
+ym000@bio001:~$ cp .ssh/id_rsa.pub .ssh/authorized_keys
+}}}
+   * [備註] '''因為是 DRBL 環境, 因此每一台都已經有 .ssh/authorized_keys''', 如果不是 DRBL 環境, 你必須要自己手動把 .ssh/id_rsa.pub 拷貝到每一台 Compute Node 的 .ssh/authorized_keys
+{{{
+ym000@bio001:~$ for ((i=2;i<=7;i++)); do scp .ssh/id_rsa.pub ym000@192.168.192.$i:.ssh/authorized_keys ; done
+}}}
+ * 設定 MPD 設定檔跟 MPI 的執行檔路徑
+{{{
+ym000@bio001:~$ echo "MPD_SECRETWORD=${user}$$" > ~/.mpd.conf
+ym000@bio001:~$ chmod 600 .mpd.conf
+ym000@bio001:~$ for ((i=2;i<=7;i++)); do echo "192.168.129.$i" >> mpd.hosts; done
+ym000@bio001:~$ export PATH=$PATH:/opt/mpich2/bin
+ym000@bio001:~$ which mpdboot
+/opt/mpich2/bin/mpdboot
+}}}
+ * 設定 dsh (distributed shell)[http://packages.debian.org/stable/net/dsh *], 我們可以使用 dsh 指令逐台執行.
+{{{
+ym000@bio001:~$ mkdir -p .dsh/
+ym000@bio001:~$ cp mpd.hosts .dsh/machines.list
+ym000@bio001:~$ dsh -a hostname
+bio001002
+bio001003
+The authenticity of host '192.168.129.4 (192.168.129.4)' can't be established.
+RSA key fingerprint is f0:4b:6f:52:3c:0b:f4:8b:1c:a0:33:4a:e2:15:e0:5a.
+Are you sure you want to continue connecting (yes/no)? yes
+Warning: Permanently added '192.168.129.4' (RSA) to the list of known hosts.
+bio001004
+The authenticity of host '192.168.129.5 (192.168.129.5)' can't be established.
+RSA key fingerprint is 09:9b:25:5e:9c:a8:9a:dd:35:ee:f0:54:6a:11:b7:90.
+Are you sure you want to continue connecting (yes/no)? yes
+Warning: Permanently added '192.168.129.5' (RSA) to the list of known hosts.
+bio001005
+The authenticity of host '192.168.129.6 (192.168.129.6)' can't be established.
+RSA key fingerprint is 40:10:50:38:2c:f0:0b:f7:11:85:a3:41:d9:fb:ac:7d.
+Are you sure you want to continue connecting (yes/no)? yes
+Warning: Permanently added '192.168.129.6' (RSA) to the list of known hosts.
+bio001006
+The authenticity of host '192.168.129.7 (192.168.129.7)' can't be established.
+RSA key fingerprint is 07:95:b7:f8:a5:9c:c7:21:84:d0:5b:f4:5f:db:0b:a6.
+Are you sure you want to continue connecting (yes/no)? yes
+Warning: Permanently added '192.168.129.7' (RSA) to the list of known hosts.
+bio001007
+ym000@bio001:~$ dsh -a hostname
+bio001002
+bio001003
+bio001004
+bio001005
+bio001006
+bio001007
+}}}
+ * 用使用者的身分執行 mpd
+{{{
+ym000@bio001:~$ mpdboot -n 7
+}}}
+ * 用 mpdtrace 檢查 mpd 執行狀態
+{{{
+ym000@bio001:~$ mpdtrace 
+bio001
+bio001005
+bio001004
+bio001003
+bio001002
+bio001007
+bio001006
+}}}
+ * 用 mpdringtest 做 mpd 訊息傳遞效能測試
+{{{
+ym000@bio001:~$ mpdringtest 1000
+time for 1000 loops = 0.648007154465 seconds
+}}}
+ * 用 mpiexec 執行 cpi 範例程式
+{{{
+ym000@bio001:~$ mpiexec -n 3 /opt/mpich2/share/mpich2/examples/cpi
+Process 0 of 1 is on bio001
+pi is approximately 3.1415926544231341, Error is 0.0000000008333410
+wall clock time = 0.000284
+Process 0 of 1 is on bio001
+pi is approximately 3.1415926544231341, Error is 0.0000000008333410
+wall clock time = 0.000295
+Process 0 of 1 is on bio001
+pi is approximately 3.1415926544231341, Error is 0.0000000008333410
+wall clock time = 0.000294
+}}}
+ * 貼上 test1.c
+{{{
+ym000@bio001:~$ cat << EOF > test1.c
+> #include <stdio.h>
+> #include <mpi.h>
+> main (int argc, char **argv)
+> {
+>   int rank, size, len;
+>   char name[MPI_MAX_PROCESSOR_NAME];
+>   MPI_Init(&argc, &argv);
+>   int myid, numprocs;
+>
+>   /* 取得 node 總數 */
+>   MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
+>   /* 取得本身 node id / rank */
+>   MPI_Comm_rank(MPI_COMM_WORLD,&myid);
+  MPI_Get_processor_name(name, &len);
+>   /* 取得本身 host name */
+>   MPI_Get_processor_name(name, &len);
+>   printf("This is machine %d of %d name = %s\n", myid, numprocs, name);
+>
+>   MPI_Finalize();
+> }
+> EOF
+}}}
+ * 用 mpicc 編譯 test1.c
+{{{
+ym000@bio001:~$ mpicc -o test1 test1.c
+}}}
+ * 用 mpiexec 執行 test1 程式
+{{{
+ym000@bio001:~$ mpiexec -n 1 ./test1
+This is machine 0 of 1 name = bio001
+ym000@bio001:~$ mpiexec -n 12 ./test1
+This is machine 0 of 12 name = bio001
+This is machine 1 of 12 name = bio001004
+This is machine 2 of 12 name = bio001005
+This is machine 3 of 12 name = bio001003
+This is machine 4 of 12 name = bio001002
+This is machine 5 of 12 name = bio001007
+This is machine 6 of 12 name = bio001006
+This is machine 7 of 12 name = bio001
+This is machine 8 of 12 name = bio001004
+This is machine 11 of 12 name = bio001002
+This is machine 9 of 12 name = bio001005
+This is machine 10 of 12 name = bio001003
+}}}
+ * here is test1.c
+{{{
+#include <stdio.h>
+#include <mpi.h>
+main (int argc, char **argv)
+{
+  int rank, size, len;
+  char name[MPI_MAX_PROCESSOR_NAME];
+  MPI_Init(&argc, &argv);
+  int myid, numprocs;
+
+  /* 取得 node 總數 */
+  MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
+  /* 取得本身 node id / rank */
+  MPI_Comm_rank(MPI_COMM_WORLD,&myid);
+  /* 取得本身 host name */
+  MPI_Get_processor_name(name, &len);
+  printf("This is machine %d of %d name = %s\n", myid, numprocs, name);
+
+  MPI_Finalize();
+}
+}}}
+ * here is test2.c
+{{{
+#include <mpi.h>
+#include <stdio.h>
+main(int argc,char **argv) { 
+  int n, myrank, numprocs;
+  MPI_Status status;
+  MPI_Init(&argc,&argv);
+  MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
+  MPI_Comm_rank(MPI_COMM_WORLD,&myrank);
+
+  /* node 0 will send the first message */
+  if(myrank == 0) {
+    n = myrank;
+    MPI_Send(&n, 1, MPI_INT, 1, 99, MPI_COMM_WORLD);
+    printf("[Ndde %d]「%d」 >> [Node %d]\n\n", myrank, n, myrank+1);
+  }
+
+  /* node 1 to node n-2 will send message to the next node */
+  if(myrank>0 && myrank<numprocs-1) {
+    MPI_Recv(&n, 1, MPI_INT, myrank-1, 99, MPI_COMM_WORLD, &status);
+    printf("[Node %d] << 「%d」[Node %d]\n", myrank, n, status.MPI_SOURCE);
+    n = myrank; MPI_Send(&n, 1, MPI_INT, myrank+1, 99, MPI_COMM_WORLD);
+    printf("[Ndde %d]「%d」 >> [Node %d]\n\n", myrank, n, myrank+1);
+  }
+
+ /* the final node n-1 will not send any message but receive*/
+  if(myrank==numprocs-1) {
+    MPI_Recv(&n, 1, MPI_INT, myrank-1, 99, MPI_COMM_WORLD, &status);
+    printf("[Node %d] << 「%d」[Node %d]\n", myrank, n, status.MPI_SOURCE);
+    }
+
+  MPI_Finalize();
+} 
+}}}
+ * here is test3.c
+{{{
+/* Program:
+ *   每個 node 將訊息傳送給 node 0，由，node 0 統一印出
+ * History:
+ *   2008-06-12 BETA
+ *   2008-06-17 更改顯示方式，並增加註解
+ */
+
+#include <stdio.h>
+#include <mpi.h>
+#include <string.h>
+
+main(int argc, char **argv)
+{
+  int myrank, i, numprocs;
+  char message[20];
+  MPI_Status status;
+  MPI_Init(&argc, &argv);
+  MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
+  MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
+
+  /* Node 0 will do the following */
+  if(myrank == 0)
+  {
+    /* receive messages from other nodes */
+    for(i = 1; i < numprocs; i++)
+    {
+      MPI_Recv(message, 20, MPI_CHAR, i, 99, MPI_COMM_WORLD, &status);
+      printf("[Node 0] << 「%s」[Node %d] \n", message, status.MPI_SOURCE);
+    }
+  }
+
+  /* other Nodes will do the following */
+  if(myrank != 0)
+  {
+    /* send node's rank to Node 0 */
+    sprintf(message, "[%d]", myrank);
+    MPI_Send(message, 20, MPI_CHAR, 0, 99, MPI_COMM_WORLD);
+    printf("[Node %d]「%s」 >> [Node 0]\n", myrank, message);
+  }
+  MPI_Finalize();
+}
+}}}
+ * here is test4
+{{{
+/* Program:
+ *   讓 node 0 可以接受來自任何 node 的訊息，每個 node 將訊息標上不同 tag 後傳給 node 0
+ * History:
+ *   2008-06-24 BETA
+ */
+
+#include <stdio.h>
+#include <mpi.h>
+
+main (int argc, char **argv)
+{
+  int numprocs, myrank, i=0, buf;
+  MPI_Status status;
+  MPI_Init(&argc, &argv);
+  MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
+  MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
+
+  /* 除了 Node 0 以外的所有 node 都要送 5 個訊息給 node 0 ， 將 i 當成 tag 送出 */
+  if (myrank > 0)
+  {
+    for(i = 0; i < 5; i++)
+    {
+      buf = myrank * 100 + i;
+      MPI_Send(&buf, 1, MPI_INT, 0, i, MPI_COMM_WORLD);
+    }
+  }
+  if (myrank == 0)
+  {
+    for (i = 0; i < 5*(numprocs-1); i++)
+    {
+
+      /* MPI_ANY_SOURCE 接收來自任何 node ， MPI_ANY_TAG 接收來自任何 tag */
+      MPI_Recv(&buf, 1, MPI_INT, MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD, &status);
+      printf("[Node %d][Tag %d] => %d\n", status.MPI_SOURCE, status.MPI_TAG, buf);
+    }
+  }
+  MPI_Finalize();
+}
+}}}