Bingo - found it, fix submitted and hope to get it into 2.0.1

Thanks for the assist!
Ralph


> On Aug 24, 2016, at 12:15 PM, Jingchao Zhang <zh...@unl.edu> wrote:
> 
> I configured v2.0.1rc1 with --enable-debug and ran the test with --mca 
> iof_base_verbose 100. I also added -display-devel-map in case it provides 
> some useful information.
> 
> Test job has 2 nodes, each node 10 cores. Rank 0 and mpirun command on the 
> same node.
> $ mpirun -display-devel-map --mca iof_base_verbose 100 ./a.out < test.in &> 
> debug_info.txt
> 
> The debug_info.txt is attached. 
> 
> Dr. Jingchao Zhang
> Holland Computing Center
> University of Nebraska-Lincoln
> 402-472-6400
> From: users <users-boun...@lists.open-mpi.org 
> <mailto:users-boun...@lists.open-mpi.org>> on behalf of r...@open-mpi.org 
> <mailto:r...@open-mpi.org> <r...@open-mpi.org <mailto:r...@open-mpi.org>>
> Sent: Wednesday, August 24, 2016 12:14:26 PM
> To: Open MPI Users
> Subject: Re: [OMPI users] stdin issue with openmpi/2.0.0
>  
> Afraid I can’t replicate a problem at all, whether rank=0 is local or not. 
> I’m also using bash, but on CentOS-7, so I suspect the OS is the difference.
> 
> Can you configure OMPI with --enable-debug, and then run the test again with 
> --mca iof_base_verbose 100? It will hopefully tell us something about why the 
> IO subsystem is stuck.
> 
> 
>> On Aug 24, 2016, at 8:46 AM, Jingchao Zhang <zh...@unl.edu 
>> <mailto:zh...@unl.edu>> wrote:
>> 
>> Hi Ralph,
>> 
>> For our tests, rank 0 is always on the same node with mpirun. I just tested 
>> mpirun with -nolocal and it still hangs. 
>> 
>> Information on shell and OS
>> $ echo $0
>> -bash
>> 
>> $ lsb_release -a
>> LSB Version:    
>> :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
>> Distributor ID: Scientific
>> Description:    Scientific Linux release 6.8 (Carbon)
>> Release:        6.8
>> Codename:       Carbon
>> 
>> $ uname -a
>> Linux login.crane.hcc.unl.edu <http://login.crane.hcc.unl.edu/> 
>> 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 11:25:51 CDT 2016 x86_64 x86_64 
>> x86_64 GNU/Linux
>> 
>> 
>> Dr. Jingchao Zhang
>> Holland Computing Center
>> University of Nebraska-Lincoln
>> 402-472-6400
>> From: users <users-boun...@lists.open-mpi.org 
>> <mailto:users-boun...@lists.open-mpi.org>> on behalf of r...@open-mpi.org 
>> <mailto:r...@open-mpi.org> <r...@open-mpi.org <mailto:r...@open-mpi.org>>
>> Sent: Tuesday, August 23, 2016 8:14:48 PM
>> To: Open MPI Users
>> Subject: Re: [OMPI users] stdin issue with openmpi/2.0.0
>>  
>> Hmmm...that’s a good point. Rank 0 and mpirun are always on the same node on 
>> my cluster. I’ll give it a try.
>> 
>> Jingchao: is rank 0 on the node with mpirun, or on a remote node?
>> 
>> 
>>> On Aug 23, 2016, at 5:58 PM, Gilles Gouaillardet <gil...@rist.or.jp 
>>> <mailto:gil...@rist.or.jp>> wrote:
>>> 
>>> Ralph,
>>> 
>>> did you run task 0 and mpirun on different nodes ?
>>> 
>>> i observed some random hangs, though i cannot blame openmpi 100% yet
>>> 
>>> Cheers,
>>> 
>>> Gilles
>>> 
>>> On 8/24/2016 9:41 AM, r...@open-mpi.org <mailto:r...@open-mpi.org> wrote:
>>>> Very strange. I cannot reproduce it as I’m able to run any number of nodes 
>>>> and procs, pushing over 100Mbytes thru without any problem.
>>>> 
>>>> Which leads me to suspect that the issue here is with the tty interface. 
>>>> Can you tell me what shell and OS you are running?
>>>> 
>>>> 
>>>>> On Aug 23, 2016, at 3:25 PM, Jingchao Zhang <zh...@unl.edu 
>>>>> <mailto:zh...@unl.edu>> wrote:
>>>>> 
>>>>> Everything stuck at MPI_Init. For a test job with 2 nodes and 10 cores 
>>>>> each node, I got the following
>>>>> 
>>>>> $ mpirun ./a.out < test.in
>>>>> Rank 2 has cleared MPI_Init
>>>>> Rank 4 has cleared MPI_Init
>>>>> Rank 7 has cleared MPI_Init
>>>>> Rank 8 has cleared MPI_Init
>>>>> Rank 0 has cleared MPI_Init
>>>>> Rank 5 has cleared MPI_Init
>>>>> Rank 6 has cleared MPI_Init
>>>>> Rank 9 has cleared MPI_Init
>>>>> Rank 1 has cleared MPI_Init
>>>>> Rank 16 has cleared MPI_Init
>>>>> Rank 19 has cleared MPI_Init
>>>>> Rank 10 has cleared MPI_Init
>>>>> Rank 11 has cleared MPI_Init
>>>>> Rank 12 has cleared MPI_Init
>>>>> Rank 13 has cleared MPI_Init
>>>>> Rank 14 has cleared MPI_Init
>>>>> Rank 15 has cleared MPI_Init
>>>>> Rank 17 has cleared MPI_Init
>>>>> Rank 18 has cleared MPI_Init
>>>>> Rank 3 has cleared MPI_Init
>>>>> 
>>>>> then it just hanged.
>>>>> 
>>>>> --Jingchao
>>>>> 
>>>>> Dr. Jingchao Zhang
>>>>> Holland Computing Center
>>>>> University of Nebraska-Lincoln
>>>>> 402-472-6400
>>>>> From: users <users-boun...@lists.open-mpi.org 
>>>>> <mailto:users-boun...@lists.open-mpi.org>> on behalf of r...@open-mpi.org 
>>>>> <mailto:r...@open-mpi.org> <r...@open-mpi.org <mailto:r...@open-mpi.org>>
>>>>> Sent: Tuesday, August 23, 2016 4:03:07 PM
>>>>> To: Open MPI Users
>>>>> Subject: Re: [OMPI users] stdin issue with openmpi/2.0.0
>>>>>  
>>>>> The IO forwarding messages all flow over the Ethernet, so the type of 
>>>>> fabric is irrelevant. The number of procs involved would definitely have 
>>>>> an impact, but that might not be due to the IO forwarding subsystem. We 
>>>>> know we have flow control issues with collectives like Bcast that don’t 
>>>>> have built-in synchronization points. How many reads were you able to do 
>>>>> before it hung?
>>>>> 
>>>>> I was running it on my little test setup (2 nodes, using only a few 
>>>>> procs), but I’ll try scaling up and see what happens. I’ll also try 
>>>>> introducing some forced “syncs” on the Bcast and see if that solves the 
>>>>> issue.
>>>>> 
>>>>> Ralph
>>>>> 
>>>>>> On Aug 23, 2016, at 2:30 PM, Jingchao Zhang <zh...@unl.edu 
>>>>>> <mailto:zh...@unl.edu>> wrote:
>>>>>> 
>>>>>> Hi Ralph,
>>>>>> 
>>>>>> I tested v2.0.1rc1 with your code but has the same issue. I also 
>>>>>> installed v2.0.1rc1 on a different cluster which has Mellanox QDR 
>>>>>> Infiniband and get the same result. For the tests you have done, how 
>>>>>> many cores and nodes did you use? I can trigger the problem by using 
>>>>>> multiple nodes and each node with more than 10 cores. 
>>>>>> 
>>>>>> Thank you for looking into this.
>>>>>> 
>>>>>> Dr. Jingchao Zhang
>>>>>> Holland Computing Center
>>>>>> University of Nebraska-Lincoln
>>>>>> 402-472-6400
>>>>>> From: users <users-boun...@lists.open-mpi.org 
>>>>>> <mailto:users-boun...@lists.open-mpi.org>> on behalf of 
>>>>>> r...@open-mpi.org <mailto:r...@open-mpi.org> <r...@open-mpi.org 
>>>>>> <mailto:r...@open-mpi.org>>
>>>>>> Sent: Monday, August 22, 2016 10:23:42 PM
>>>>>> To: Open MPI Users
>>>>>> Subject: Re: [OMPI users] stdin issue with openmpi/2.0.0
>>>>>>  
>>>>>> FWIW: I just tested forwarding up to 100MBytes via stdin using the 
>>>>>> simple test shown below with OMPI v2.0.1rc1, and it worked fine. So I’d 
>>>>>> suggest upgrading when the official release comes out, or going ahead 
>>>>>> and at least testing 2.0.1rc1 on your machine. Or you can test this 
>>>>>> program with some input file and let me know if it works for you.
>>>>>> 
>>>>>> Ralph
>>>>>> 
>>>>>> #include <stdlib.h>
>>>>>> #include <stdio.h>
>>>>>> #include <string.h>
>>>>>> #include <stdbool.h>
>>>>>> #include <unistd.h>
>>>>>> #include <mpi.h>
>>>>>> 
>>>>>> #define ORTE_IOF_BASE_MSG_MAX   2048
>>>>>> 
>>>>>> int main(int argc, char *argv[])
>>>>>> {
>>>>>>     int i, rank, size, next, prev, tag = 201;
>>>>>>     int pos, msgsize, nbytes;
>>>>>>     bool done;
>>>>>>     char *msg;
>>>>>> 
>>>>>>     MPI_Init(&argc, &argv);
>>>>>>     MPI_Comm_rank(MPI_COMM_WORLD, &rank);
>>>>>>     MPI_Comm_size(MPI_COMM_WORLD, &size);
>>>>>> 
>>>>>>     fprintf(stderr, "Rank %d has cleared MPI_Init\n", rank);
>>>>>> 
>>>>>>     next = (rank + 1) % size;
>>>>>>     prev = (rank + size - 1) % size;
>>>>>>     msg = malloc(ORTE_IOF_BASE_MSG_MAX);
>>>>>>     pos = 0;
>>>>>>     nbytes = 0;
>>>>>> 
>>>>>>     if (0 == rank) {
>>>>>>         while (0 != (msgsize = read(0, msg, ORTE_IOF_BASE_MSG_MAX))) {
>>>>>>             fprintf(stderr, "Rank %d: sending blob %d\n", rank, pos);
>>>>>>             if (msgsize > 0) {
>>>>>>                 MPI_Bcast(msg, ORTE_IOF_BASE_MSG_MAX, MPI_BYTE, 0, 
>>>>>> MPI_COMM_WORLD);
>>>>>>             }
>>>>>>             ++pos;
>>>>>>             nbytes += msgsize;
>>>>>>         }
>>>>>>         fprintf(stderr, "Rank %d: sending termination blob %d\n", rank, 
>>>>>> pos);
>>>>>>         memset(msg, 0, ORTE_IOF_BASE_MSG_MAX);
>>>>>>         MPI_Bcast(msg, ORTE_IOF_BASE_MSG_MAX, MPI_BYTE, 0, 
>>>>>> MPI_COMM_WORLD);
>>>>>>         MPI_Barrier(MPI_COMM_WORLD);
>>>>>>     } else {
>>>>>>         while (1) {
>>>>>>             MPI_Bcast(msg, ORTE_IOF_BASE_MSG_MAX, MPI_BYTE, 0, 
>>>>>> MPI_COMM_WORLD);
>>>>>>             fprintf(stderr, "Rank %d: recvd blob %d\n", rank, pos);
>>>>>>             ++pos;
>>>>>>             done = true;
>>>>>>             for (i=0; i < ORTE_IOF_BASE_MSG_MAX; i++) {
>>>>>>                 if (0 != msg[i]) {
>>>>>>                     done = false;
>>>>>>                     break;
>>>>>>                 }
>>>>>>             }
>>>>>>             if (done) {
>>>>>>                 break;
>>>>>>             }
>>>>>>         }
>>>>>>         fprintf(stderr, "Rank %d: recv done\n", rank);
>>>>>>         MPI_Barrier(MPI_COMM_WORLD);
>>>>>>     }
>>>>>> 
>>>>>>     fprintf(stderr, "Rank %d has completed bcast\n", rank);
>>>>>>     MPI_Finalize();
>>>>>>     return 0;
>>>>>> }
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On Aug 22, 2016, at 3:40 PM, Jingchao Zhang <zh...@unl.edu 
>>>>>>> <mailto:zh...@unl.edu>> wrote:
>>>>>>> 
>>>>>>> This might be a thin argument but we have many users running mpirun in 
>>>>>>> this way for years with no problem until this recent upgrade. And some 
>>>>>>> home-brewed mpi codes do not even have a standard way to read the input 
>>>>>>> files. Last time I checked, the openmpi manual still claims it supports 
>>>>>>> stdin (https://www.open-mpi.org/doc/v2.0/man1/mpirun.1.php#sect14 
>>>>>>> <https://www.open-mpi.org/doc/v2.0/man1/mpirun.1.php#sect14>). Maybe I 
>>>>>>> missed it but the v2.0 release notes did not mention any changes to the 
>>>>>>> behaviors of stdin as well.
>>>>>>> 
>>>>>>> We can tell our users to run mpirun in the suggested way, but I do hope 
>>>>>>> someone can look into the issue and fix it.
>>>>>>> 
>>>>>>> Dr. Jingchao Zhang
>>>>>>> Holland Computing Center
>>>>>>> University of Nebraska-Lincoln
>>>>>>> 402-472-6400
>>>>>>> From: users <users-boun...@lists.open-mpi.org 
>>>>>>> <mailto:users-boun...@lists.open-mpi.org>> on behalf of 
>>>>>>> r...@open-mpi.org <mailto:r...@open-mpi.org> <r...@open-mpi.org 
>>>>>>> <mailto:r...@open-mpi.org>>
>>>>>>> Sent: Monday, August 22, 2016 3:04:50 PM
>>>>>>> To: Open MPI Users
>>>>>>> Subject: Re: [OMPI users] stdin issue with openmpi/2.0.0
>>>>>>>  
>>>>>>> Well, I can try to find time to take a look. However, I will reiterate 
>>>>>>> what Jeff H said - it is very unwise to rely on IO forwarding. Much 
>>>>>>> better to just directly read the file unless that file is simply 
>>>>>>> unavailable on the node where rank=0 is running.
>>>>>>> 
>>>>>>>> On Aug 22, 2016, at 1:55 PM, Jingchao Zhang <zh...@unl.edu 
>>>>>>>> <mailto:zh...@unl.edu>> wrote:
>>>>>>>> 
>>>>>>>> Here you can find the source code for lammps input 
>>>>>>>> https://github.com/lammps/lammps/blob/r13864/src/input.cpp 
>>>>>>>> <https://github.com/lammps/lammps/blob/r13864/src/input.cpp>
>>>>>>>> Based on the gdb output, rank 0 stuck at line 167
>>>>>>>> if
>>>>>>>>  (fgets(&line[m],maxline-m,infile)
>>>>>>>>  == NULL)
>>>>>>>> and the rest threads stuck at line 203
>>>>>>>> MPI_Bcast(&n,1,MPI_INT,0,world);
>>>>>>>> 
>>>>>>>> So rank 0 possibly hangs on the fgets() function.
>>>>>>>> 
>>>>>>>> Here are the whole backtrace information:
>>>>>>>> $ cat master.backtrace worker.backtrace
>>>>>>>> #0  0x0000003c37cdb68d in read () from /lib64/libc.so.6
>>>>>>>> #1  0x0000003c37c71ca8 in _IO_new_file_underflow () from 
>>>>>>>> /lib64/libc.so.6
>>>>>>>> #2  0x0000003c37c737ae in _IO_default_uflow_internal () from 
>>>>>>>> /lib64/libc.so.6
>>>>>>>> #3  0x0000003c37c67e8a in _IO_getline_info_internal () from 
>>>>>>>> /lib64/libc.so.6
>>>>>>>> #4  0x0000003c37c66ce9 in fgets () from /lib64/libc.so.6
>>>>>>>> #5  0x00000000005c5a43 in LAMMPS_NS::Input::file() () at 
>>>>>>>> ../input.cpp:167
>>>>>>>> #6  0x00000000005d4236 in main () at ../main.cpp:31
>>>>>>>> #0  0x00002b1635d2ace2 in poll_dispatch () from 
>>>>>>>> /util/opt/openmpi/2.0.0/gcc/6.1.0/lib/libopen-pal.so.20
>>>>>>>> #1  0x00002b1635d1fa71 in opal_libevent2022_event_base_loop ()
>>>>>>>>    from /util/opt/openmpi/2.0.0/gcc/6.1.0/lib/libopen-pal.so.20
>>>>>>>> #2  0x00002b1635ce4634 in opal_progress () from 
>>>>>>>> /util/opt/openmpi/2.0.0/gcc/6.1.0/lib/libopen-pal.so.20
>>>>>>>> #3  0x00002b16351b8fad in ompi_request_default_wait () from 
>>>>>>>> /util/opt/openmpi/2.0.0/gcc/6.1.0/lib/libmpi.so.20
>>>>>>>> #4  0x00002b16351fcb40 in ompi_coll_base_bcast_intra_generic ()
>>>>>>>>    from /util/opt/openmpi/2.0.0/gcc/6.1.0/lib/libmpi.so.20
>>>>>>>> #5  0x00002b16351fd0c2 in ompi_coll_base_bcast_intra_binomial ()
>>>>>>>>    from /util/opt/openmpi/2.0.0/gcc/6.1.0/lib/libmpi.so.20
>>>>>>>> #6  0x00002b1644fa6d9b in ompi_coll_tuned_bcast_intra_dec_fixed ()
>>>>>>>>    from /util/opt/openmpi/2.0.0/gcc/6.1.0/lib/openmpi/mca_coll_tuned.so
>>>>>>>> #7  0x00002b16351cb4fb in PMPI_Bcast () from 
>>>>>>>> /util/opt/openmpi/2.0.0/gcc/6.1.0/lib/libmpi.so.20
>>>>>>>> #8  0x00000000005c5b5d in LAMMPS_NS::Input::file() () at 
>>>>>>>> ../input.cpp:203
>>>>>>>> #9  0x00000000005d4236 in main () at ../main.cpp:31
>>>>>>>> 
>>>>>>>> Thanks,
>>>>>>>> 
>>>>>>>> Dr. Jingchao Zhang
>>>>>>>> Holland Computing Center
>>>>>>>> University of Nebraska-Lincoln
>>>>>>>> 402-472-6400
>>>>>>>> From: users <users-boun...@lists.open-mpi.org 
>>>>>>>> <mailto:users-boun...@lists.open-mpi.org>> on behalf of 
>>>>>>>> r...@open-mpi.org <mailto:r...@open-mpi.org> <r...@open-mpi.org 
>>>>>>>> <mailto:r...@open-mpi.org>>
>>>>>>>> Sent: Monday, August 22, 2016 2:17:10 PM
>>>>>>>> To: Open MPI Users
>>>>>>>> Subject: Re: [OMPI users] stdin issue with openmpi/2.0.0
>>>>>>>>  
>>>>>>>> Hmmm...perhaps we can break this out a bit? The stdin will be going to 
>>>>>>>> your rank=0 proc. It sounds like you have some subsequent step that 
>>>>>>>> calls MPI_Bcast?
>>>>>>>> 
>>>>>>>> Can you first verify that the input is being correctly delivered to 
>>>>>>>> rank=0? This will help us isolate if the problem is in the IO 
>>>>>>>> forwarding, or in the subsequent Bcast.
>>>>>>>> 
>>>>>>>>> On Aug 22, 2016, at 1:11 PM, Jingchao Zhang <zh...@unl.edu 
>>>>>>>>> <mailto:zh...@unl.edu>> wrote:
>>>>>>>>> 
>>>>>>>>> Hi all,
>>>>>>>>> 
>>>>>>>>> We compiled openmpi/2.0.0 with gcc/6.1.0 and intel/13.1.3. Both of 
>>>>>>>>> them have odd behaviors when trying to read from standard input.
>>>>>>>>> 
>>>>>>>>> For example, if we start the application lammps across 4 nodes, each 
>>>>>>>>> node 16 cores, connected by Intel QDR Infiniband, mpirun works fine 
>>>>>>>>> for the 1st time, but always stuck in a few seconds thereafter.
>>>>>>>>> Command:
>>>>>>>>> mpirun ./lmp_ompi_g++ < in.snr
>>>>>>>>> in.snr is the Lammps input file. compiler is gcc/6.1.
>>>>>>>>> 
>>>>>>>>> Instead, if we use
>>>>>>>>> mpirun ./lmp_ompi_g++ -in in.snr
>>>>>>>>> it works 100%.
>>>>>>>>> 
>>>>>>>>> Some odd behaviors we gathered so far. 
>>>>>>>>> 1. For 1 node job, stdin always works.
>>>>>>>>> 2. For multiple nodes, stdin works unstably when the number of cores 
>>>>>>>>> per node are relatively small. For example, for 2/3/4 nodes, each 
>>>>>>>>> node 8 cores, mpirun works most of the time. But for each node with 
>>>>>>>>> >8 cores, mpirun works the 1st time, then always stuck. There seems 
>>>>>>>>> to be a magic number when it stops working.
>>>>>>>>> 3. We tested Quantum Expresso with compiler intel/13 and had the same 
>>>>>>>>> issue. 
>>>>>>>>> 
>>>>>>>>> We used gdb to debug and found when mpirun was stuck, the rest of the 
>>>>>>>>> processes were all waiting on mpi broadcast from the master thread. 
>>>>>>>>> The lammps binary, input file and gdb core files (example.tar.bz2) 
>>>>>>>>> can be downloaded from this link 
>>>>>>>>> https://drive.google.com/open?id=0B3Yj4QkZpI-dVWZtWmJ3ZXNVRGc 
>>>>>>>>> <https://drive.google.com/open?id=0B3Yj4QkZpI-dVWZtWmJ3ZXNVRGc>
>>>>>>>>> 
>>>>>>>>> Extra information:
>>>>>>>>> 1. Job scheduler is slurm.
>>>>>>>>> 2. configure setup:
>>>>>>>>> ./configure     --prefix=$PREFIX \
>>>>>>>>>                 --with-hwloc=internal \
>>>>>>>>>                 --enable-mpirun-prefix-by-default \
>>>>>>>>>                 --with-slurm \
>>>>>>>>>                 --with-verbs \
>>>>>>>>>                 --with-psm \
>>>>>>>>>                 --disable-openib-connectx-xrc \
>>>>>>>>>                 --with-knem=/opt/knem-1.1.2.90mlnx1 \
>>>>>>>>>                 --with-cma
>>>>>>>>> 3. openmpi-mca-params.conf file 
>>>>>>>>> orte_hetero_nodes=1
>>>>>>>>> hwloc_base_binding_policy=core
>>>>>>>>> rmaps_base_mapping_policy=core
>>>>>>>>> opal_cuda_support=0
>>>>>>>>> btl_openib_use_eager_rdma=0
>>>>>>>>> btl_openib_max_eager_rdma=0
>>>>>>>>> btl_openib_flags=1
>>>>>>>>> 
>>>>>>>>> Thanks,
>>>>>>>>> Jingchao 
>>>>>>>>> 
>>>>>>>>> Dr. Jingchao Zhang
>>>>>>>>> Holland Computing Center
>>>>>>>>> University of Nebraska-Lincoln
>>>>>>>>> 402-472-6400
>>>>>>>>> _______________________________________________
>>>>>>>>> users mailing list
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>>>>>>>>> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users>
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