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<p class="MsoNormal">I am having problems in one my project related to MPI development. I am working on the implementation of an RNA parsing algorithm using MPI in which I started the parsing of an input string based on some parsing rules and parsing table
(contains different states and related actions) with a master node. In parsing table, there are multiple actions for each state which can be done in parallel. So, I have to distribute these actions among different processes. To do that, I am sending the current
state and parsing info (current stack of parsing) to the nodes using separate thread to receive actions from other nodes while the main thread is busy in parsing based on received actions. Following are the code snippets of the sender and receiver:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="border:none;padding:0in">Sender Code:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt">StackFlush(&snd_stack);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">StackPush(&snd_stack, state_index);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">StackPush(&snd_stack, current_ch);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">StackPush(&snd_stack, actions_to_skip);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">elements_in_stack = stack.top + 1;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">for(int a=elements_in_stack-1;a>=0;a--)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt"> StackPush(&snd_stack, stack.contents[a]);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">StackPush(&snd_stack, elements_in_stack);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">elements_in_stack = parse_tree.top + 1;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">for(int a=elements_in_stack-1;a>=0;a--)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt"> StackPush(&snd_stack, parse_tree.contents[a]);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">StackPush(&snd_stack, elements_in_stack);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">elements_in_stack = snd_stack.top+1;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">MPI_Send(&elements_in_stack, 1, MPI_INT, (myrank + actions_to_skip) % mysize, MSG_ACTION_STACK_COUNT, MPI_COMM_WORLD);<o:p></o:p></span></p>
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<p class="MsoNormal" style="border:none;padding:0in"><span style="font-size:9.0pt">MPI_Send(&snd_stack.contents[0], elements_in_stack, MPI_CHAR, (myrank + actions_to_skip) % mysize, MSG_ACTION_STACK, MPI_COMM_WORLD);<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="border:none;padding:0in">Receiver Code:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt">MPI_Recv(&e_count, 1, MPI_INT, MPI_ANY_SOURCE, MSG_ACTION_STACK_COUNT, MPI_COMM_WORLD, &status);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">if(e_count == 0){<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt"> break;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">while((bt_stack.top + e_count) >= bt_stack.maxSize - 1){usleep(500);}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">pthread_mutex_lock(&mutex_bt_stack); //using mutex for accessing shared data among threads<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">MPI_Recv(&bt_stack.contents[bt_stack.top + 1], e_count, MPI_CHAR, status.MPI_SOURCE, MSG_ACTION_STACK, MPI_COMM_WORLD, &status);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt">bt_stack.top += e_count;<o:p></o:p></span></p>
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<p class="MsoNormal" style="border:none;padding:0in"><span style="font-size:9.0pt">pthread_mutex_unlock(&mutex_bt_stack);<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="border:none;padding:0in">The program is running fine for small input having less communications but as we increase the input size which in response increases the communication so the receiver receives many requests while processing
few then it get crashed with the following errors:<o:p></o:p></p>
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<p class="MsoNormal">Fatal error in MPI_Recv: Message truncated, error stack:<o:p></o:p></p>
<p class="MsoNormal">MPI_Recv(186) ……………………………………: MPI_Recv(buf=0x5b8d7b1, count=19, MPI_CHAR, src=3, tag=1, MPI_COMM_WORLD, status=0x41732100) failed<o:p></o:p></p>
<p class="MsoNormal">MPIDI_CH3U_Request_unpack_uebuf(625)L Message truncated; 21 bytes received but buffer size is 19<o:p></o:p></p>
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<p class="MsoNormal" style="border:none;padding:0in">Rank 0 in job 73 hpc081_56549 caused collective abort of all ranks exit status of rank 0: killed by signal 9.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have also tried this by using Non-Blocking MPI calls but still the similar errors.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="color:#1F497D">Ayaz ul Hassan Khan<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Lecturer-B (PhD Student), Information and Computer Sciences<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">King Fahd University of Petroleum & Minerals<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Dhahran 31261, Kingdom of Saudi Arabia<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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