Michael,
Per the specifications, MPI_Pack_external and MPI_Unpack_external
must pack/unpack to/from big endian, regardless the endianness of the host.
On a little endian system, byte swapping must occur because this is what
you are explicitly requesting.
These functions are really meant to be used in order to write a buffer to a
file, so it can be read on an other arch, and potentially with an other MPI
library (see the man page)
Today, this is not the case and these are two bugs.
1. with --enable-heterogeneous, MPI_Pack_external does not do any byte
swapping on little endian arch, so your test fails.
2. without --enable-heterogeneous, nor MPI_Pack_external nor
MPI_Unpack_external does any byte swapping. Even if your test is working
fine, keep in mind the buffer is not in big endian format, and should not
be dumped into a file if you plan to read it later with a bug free
MPI_Unpack_external.
Once the bugs are fixed,
If you want to run on a heterogeneous cluster, you have to
- configure with --enable-heterogeneous
- use MPI_Pack_external and MPI_unpack_external if you want to pack a
message, send it to an other host with type MPI_PACKED, and unpack it there.
- not use MPI_Pack/MPI_Unpack to send/recv messages between hosts with
different endianness.
If you are only transferring predefined and derived datatypes, you have
nothing to do,
Openmpi will automatically swap bytes on the receiver side if needed.
If you want to run on a homogeneous system, you do not need
--enable-heterogeneous, and you can use MPI_Pack/MPI_Unpack, that is more
efficient than MPI_Pack_external/MPI_Unpack_external to send/recv messages.
For the time being, you are not able to write portable data with
MPI_Pack_external.
The easiest way is to run on a homogeneous cluster, configure openmpi
without --enable-heterogeneous and without --enable-debug, so pack/unpack
will work regardless you use the external or the non external subroutines.
Generally speaking, I recommend you use derived datatypes instead of
manually packing/unpacking data to/from buffers.
Cheers,
Gilles
On Friday, February 12, 2016, Michael Rezny <michael.re...@monash.edu>
wrote:
> Hi Gilles,
> I am misunderstanding something here. What you are now saying seems, to
> me, to be at odds with what you said previously.
>
> Assume the situation where both sender and receiver are little-endian, and
> discussing only MPI_Pack_external, and MPI_Unpack_external
>
> Consider case 1 --enable-heterogeneous:
> In your previous email I understood that "receiver make right" was being
> implemented
> So, sender does not byte-swap, and message is sent in (native)
> little-endian format.
> Receiver recognises the received message is in little-endian format and
> since this is also its native format, no byte swap is needed.
>
> Consider case 2 --disable-heterogeneous
> It seems strange, that, in this case, any byte swapping would ever need to
> occur.
> One is assuming a homogeneous system and sender and receiver will always
> be using their native format.
> i.e, exactly the same as MPI_Pack and MPI_Unpack.
>
> kindest regards
> Mike
>
> On 12/02/2016, at 9:25 PM, Gilles Gouaillardet wrote:
>
> Michael,
>
> byte swapping only occurs if you invoke MPI_Pack_external and
> MPI_Unpack_external on little endianness systems.
>
> MPI_Pack and MPI_Unpack uses the same engine that MPI_Send and MPI_Recv
> and this does not involve any byte swapping if both ends have the same
> endianness.
>
> Cheers,
>
> Gilles
>
> On Friday, February 12, 2016, Michael Rezny <michael.re...@monash.edu
> <javascript:_e(%7B%7D,'cvml','michael.re...@monash.edu');>> wrote:
>
>> Hi,
>> oh, that is good news! The process is meant to be implementing "receiver
>> makes right" which is good news for efficiency.
>>
>> But, in the second case, without --enable-heterogeneous, are you saying
>> that on little-endian machines, byte swapping
>> is meant to always occur? That seems most odd. I would have thought that
>> if one only wants to work and then to configure
>> OpenMPI for this mode, then there is no need to check at the receiving
>> end whether byte-swapping is needed or not. It will be assumed
>> that both sender and receiver are agreed on the format, whatever it is.
>> On a homogeneous little-endian HPC cluster one would not want
>> the extra overhead of two conversions for every packed message.
>>
>> Is it possible that the assert has been implemented incorrectly in this
>> case?
>>
>> There is absolutely no urgency with regard to a fix. Thanks to your quick
>> response, we now understand what is causing
>> the problem and are in the process of implementing a test in ./configure
>> to determine if the bug is present, and if so,
>> add a compiler flag to switch to using MPI_Pack and MPI_Unpack.
>>
>> It would be good if you would be kind enough to let me know when a fix is
>> available and I will download, build,
>> and test it on our application. Then this version can be installed as the
>> default.
>>
>> Once again, many thanks for your prompt and most helpful responses.
>>
>> warmest regards
>> MIke
>>
>> On 12/02/2016, at 7:03 PM, Gilles Gouaillardet wrote:
>>
>> Michael,
>>
>> i'd like to correct what i wrote earlier
>>
>> in heterogeneous clusters, data is sent "as is" (e.g. no byte swapping)
>> and it is byte swapped when received and only if needed.
>>
>> with --enable-heterogeneous, MPI_Unpack_external is working, but
>> MPI_Pack_external is broken
>> (e.g. no byte swapping occurs on little endian arch) since we internall
>> use the similar mechanism used to send data. that is a bug and i will work
>> on that.
>>
>> without --enable-heterogeneous, MPI_Pack_external nor MPI_Unpack_external
>> do any byte swapping and they
>> are both broken. fwiw, it you configure'd with --enable-debug, you would
>> have ran into an assert error (e.g. crash).
>>
>> i will work on a fix, but it might take some time before it is ready
>>
>> Cheers,
>>
>> Gilles
>> On 2/11/2016 6:16 PM, Gilles Gouaillardet wrote:
>>
>> Michael,
>>
>> MPI_Pack_external must convert data to big endian, so it can be dumped
>> into a file, and be read correctly on big and little endianness arch, and
>> with any MPI flavor.
>>
>> if you use only one MPI library on one arch, or if data is never
>> read/written from/to a file, then it is more efficient to MPI_Pack.
>>
>> openmpi is optimized and the data is swapped only when needed.
>> so if your cluster is little endian only, MPI_Send and MPI_Recv will
>> never byte swap data internally.
>> if both ends have different endianness, data is sent in big endian format
>> and byte swapped when received only if needed.
>> generally speaking, a send/recv requires zero or one byte swap.
>>
>> fwiw, we previously had a claim that debian nor Ubuntu have a maintainer
>> for openmpi, which would explain why an obsolete version is shipped. I made
>> a few researchs and could not find any evidence openmpi is no more
>> maintained.
>>
>> Cheers,
>>
>> Gilles
>>
>>
>>
>> On Thursday, February 11, 2016, Michael Rezny <michael.re...@monash.edu>
>> wrote:
>>
>>> Hi Gilles,
>>> thanks for thinking about this in more detail.
>>>
>>> I understand what you are saying, but your comments raise some questions
>>> in my mind:
>>>
>>> If one is in a homogeneous cluster, is it important that, in the case of
>>> little-endian, that the data be
>>> converted to extern32 format (big-endian), only to be always converted
>>> at the receiving rank
>>> back to little-endian?
>>>
>>> This would seem to be inefficient, especially if the site has no need
>>> for external MPI access.
>>>
>>> So, does --enable-heterogeneous do more than put MPI routines using
>>> "extern32" into straight pass-through?
>>>
>>> Back in the old days of PVM, all messages were converted into network
>>> order. This had severe performance impacts
>>> on little-endian clusters.
>>>
>>> So much so that a clever way of getting around this was an
>>> implementation of "receiver makes right" in which
>>> all data was sent in the native format of the sending rank. The
>>> receiving rank analysed the message to determine if
>>> a conversion was necessary. In those days with Cray format data, it
>>> could be more complicated than just byte swapping.
>>>
>>> So in essence, how is a balance struck between supporting heterogenous
>>> architectures and maximum performance
>>> with codes where message passing performance is critical?
>>>
>>> As a follow up, since I am now at home, this same problem also exists
>>> with the Ubuntu 15.10 OpenMP packages
>>> which surprisingly are still at 1.6.5, same as 14.04.
>>>
>>> Again, downloading, building, and using the latest stable version of
>>> OpenMP solved the problem.
>>>
>>> kindest regards
>>> Mike
>>>
>>>
>>> On 11/02/2016, at 7:31 PM, Gilles Gouaillardet wrote:
>>>
>>> Michael,
>>>
>>> I think it is worst than that ...
>>>
>>> without --enable-heterogeneous, it seems the data is not correctly packed
>>> (e.g. it is not converted to big endian), at least on a x86_64 arch.
>>> unpack looks broken too, but pack followed by unpack does work.
>>> that means if you are reading data correctly written in external32e
>>> format,
>>> it will not be correctly unpacked.
>>>
>>> with --enable-heterogeneous, it is only half broken
>>> (I do not know yet whether pack or unpack is broken ...)
>>> and pack followed by unpack does not work.
>>>
>>> I will double check that tomorrow
>>>
>>> Cheers,
>>>
>>> Gilles
>>>
>>> On Thursday, February 11, 2016, Michael Rezny <michael.re...@monash.edu>
>>> wrote:
>>>
>>>> Hi Ralph,
>>>> you are indeed correct. However, many of our users
>>>> have workstations such as me, with OpenMPI provided by installing a
>>>> package.
>>>> So we don't know what has been configured.
>>>>
>>>> Then we have failures, since, for instance, Ubuntu 14.04 by default
>>>> appears to have been built
>>>> with heterogeneous support! The other (working) machine is a large HPC,
>>>> and it seems OpenMPI was built
>>>> without heterogeneous support.
>>>>
>>>> Currently we work around the problem for packing and unpacking by
>>>> having a compiler switch
>>>> that will switch between calls to pack/unpack_external and pac/unpack.
>>>>
>>>> It is only now we started to track down what the problem actually is.
>>>>
>>>> kindest regards
>>>> Mike
>>>>
>>>> On 11 February 2016 at 15:54, Ralph Castain <r...@open-mpi.org> wrote:
>>>>
>>>>> Out of curiosity: if both systems are Intel, they why are you enabling
>>>>> hetero? You don’t need it in that scenario.
>>>>>
>>>>> Admittedly, we do need to fix the bug - just trying to understand why
>>>>> you are configuring that way.
>>>>>
>>>>>
>>>>> On Feb 10, 2016, at 8:46 PM, Michael Rezny <michael.re...@monash.edu>
>>>>> wrote:
>>>>>
>>>>> Hi Gilles,
>>>>> I can confirm that with a fresh download and build from source for
>>>>> OpenMPI 1.10.2
>>>>> with --enable-heterogeneous
>>>>> the unpacked ints are the wrong endian.
>>>>>
>>>>> However, without --enable-heterogeneous, the unpacked ints are correct.
>>>>>
>>>>> So, this problem still exists in heterogeneous builds with OpenMPI
>>>>> version 1.10.2.
>>>>>
>>>>> kindest regards
>>>>> Mike
>>>>>
>>>>> On 11 February 2016 at 14:48, Gilles Gouaillardet <
>>>>> gilles.gouaillar...@gmail.com> wrote:
>>>>>
>>>>>> Michael,
>>>>>>
>>>>>> does your two systems have the same endianness ?
>>>>>>
>>>>>> do you know how openmpi was configure'd on both systems ?
>>>>>> (is --enable-heterogeneous enabled or disabled on both systems ?)
>>>>>>
>>>>>> fwiw, openmpi 1.6.5 is old now and no more maintained.
>>>>>> I strongly encourage you to use openmpi 1.10.2
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Gilles
>>>>>>
>>>>>> On Thursday, February 11, 2016, Michael Rezny <
>>>>>> michael.re...@monash.edu> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>> I am running Ubuntu 14.04 LTS with OpenMPI 1.6.5 and gcc 4.8.4
>>>>>>>
>>>>>>> On a single rank program which just packs and unpacks two ints using
>>>>>>> MPI_Pack_external and MPI_Unpack_external
>>>>>>> the unpacked ints are in the wrong endian order.
>>>>>>>
>>>>>>> However, on a HPC, (not Ubuntu), using OpenMPI 1.6.5 and gcc 4.8.4
>>>>>>> the unpacked ints are correct.
>>>>>>>
>>>>>>> Is it possible to get some assistance to track down what is going on?
>>>>>>>
>>>>>>> Here is the output from the program:
>>>>>>>
>>>>>>> ~/tests/mpi/Pack test1
>>>>>>> send data 000004d2 0000162e
>>>>>>> MPI_Pack_external: 0
>>>>>>> buffer size: 8
>>>>>>> MPI_unpack_external: 0
>>>>>>> recv data d2040000 2e160000
>>>>>>>
>>>>>>> And here is the source code:
>>>>>>>
>>>>>>> #include <stdio.h>
>>>>>>> #include <mpi.h>
>>>>>>>
>>>>>>> int main(int argc, char *argv[]) {
>>>>>>> int numRanks, myRank, error;
>>>>>>>
>>>>>>> int send_data[2] = {1234, 5678};
>>>>>>> int recv_data[2];
>>>>>>>
>>>>>>> MPI_Aint buffer_size = 1000;
>>>>>>> char buffer[buffer_size];
>>>>>>>
>>>>>>> MPI_Init(&argc, &argv);
>>>>>>> MPI_Comm_size(MPI_COMM_WORLD, &numRanks);
>>>>>>> MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
>>>>>>>
>>>>>>> printf("send data %08x %08x \n", send_data[0], send_data[1]);
>>>>>>>
>>>>>>> MPI_Aint position = 0;
>>>>>>> error = MPI_Pack_external("external32", (void*) send_data, 2,
>>>>>>> MPI_INT,
>>>>>>> buffer, buffer_size, &position);
>>>>>>> printf("MPI_Pack_external: %d\n", error);
>>>>>>>
>>>>>>> printf("buffer size: %d\n", (int) position);
>>>>>>>
>>>>>>> position = 0;
>>>>>>> error = MPI_Unpack_external("external32", buffer, buffer_size,
>>>>>>> &position,
>>>>>>> recv_data, 2, MPI_INT);
>>>>>>> printf("MPI_unpack_external: %d\n", error);
>>>>>>>
>>>>>>> printf("recv data %08x %08x \n", recv_data[0], recv_data[1]);
>>>>>>>
>>>>>>> MPI_Finalize();
>>>>>>>
>>>>>>> return 0;
>>>>>>> }
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>
>>>>>
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