Re: [OMPI users] hwloc, OpenMPI and unsupported OSes and toolchains
Yes, I was going to aggregate some of the conversations that I have had (four of them, thank you much for the responses). The consensus was that neither hwloc nor OpenMPI were appropriate for my project. The use of shared memory was proposed by Jeff Squyres and one other person. From there is it a matter of deciding between interrupt driven messaging or semaphores. This (apparently unpublished) paper discusses the pros and cons of each: http://cs.brown.edu/people/irina/papers/2013-opodis.pdf One of the first approaches they discuss is Barrelfish OS, which looks to be comparable to an exokernel running an image of the OS on each CPU node: http://www.barrelfish.org/ This appears to have a robust shared memory approach. I'm still digesting the details, but it looks to solve many of the problems I am looking at. Thanks again for the discussions! tim Jeff Squyres (jsquyres) wrote: To follow up for the web thread: I talked with Tim about this off-list. Not only will Open MPI likely not work in Tim's environment, MPI itself is probably too much for what he's trying to do. On Mar 21, 2018, at 10:49 PM, Ralph H Castain wrote: I don’t see how Open MPI can operate without pthreads On Mar 19, 2018, at 3:23 PM, Gregory (tim) Kelly wrote: Hello Everyone, I'm inquiring to find someone that can answer some multi-part questions about hwloc, OpenMPI and an alternative OS and toolchain. I have a project as part of my PhD work, and it's not a simple, one-part question. For brevity, I am omitting details about the OS and toolchain, other than that neither are supported. If forced to choose between OpenMPI and the OS/toolchain, I am likely to choose the OS/toolchain and pursue other avenues for parallelization. That's part of what I am trying to determine with my inquiry. To summarize some of the question areas: 1) The OS I am working with does not support MP 2) nor does it support pthreads 3) the hardware is quad-core SoC with an integrated memory controller 4) I'd like to see if it possible to utilize hwloc and shmem to build an asymmetric multi-processing system where only one core has I/O but the other three can run the executable This is a fairly dedicated system to be used for analyzing ODEs (disease models). The hardware is cheap ($200) and uses very little power (can run off a 12v battery), and the toolchain and OS are all BSD-licensed (and everything will be published under that license). If someone is available for off-line discussion (to minimize unnecessary traffic to the list), I'd be more than willing to summarize the conversation and contribute it to the online documentation. Thank you, tim -- "Nuclear power is a hell of a way to boil water." -- Albert Einstein ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users -- Those that cast the votes decide nothing. Those that count the votes decide everything. -- Joseph Stalin ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
Re: [OMPI users] hwloc, OpenMPI and unsupported OSes and toolchains
To follow up for the web thread: I talked with Tim about this off-list. Not only will Open MPI likely not work in Tim's environment, MPI itself is probably too much for what he's trying to do. > On Mar 21, 2018, at 10:49 PM, Ralph H Castain wrote: > > I don’t see how Open MPI can operate without pthreads > >> On Mar 19, 2018, at 3:23 PM, Gregory (tim) Kelly wrote: >> >> Hello Everyone, >> I'm inquiring to find someone that can answer some multi-part questions >> about hwloc, OpenMPI and an alternative OS and toolchain. I have a project >> as part of my PhD work, and it's not a simple, one-part question. For >> brevity, I am omitting details about the OS and toolchain, other than that >> neither are supported. If forced to choose between OpenMPI and the >> OS/toolchain, I am likely to choose the OS/toolchain and pursue other >> avenues for parallelization. That's part of what I am trying to determine >> with my inquiry. >> >> To summarize some of the question areas: >> >> 1) The OS I am working with does not support MP >> 2) nor does it support pthreads >> 3) the hardware is quad-core SoC with an integrated memory controller >> 4) I'd like to see if it possible to utilize hwloc and shmem to build an >> asymmetric multi-processing system where only one core has I/O but the other >> three can run the executable >> >> This is a fairly dedicated system to be used for analyzing ODEs (disease >> models). The hardware is cheap ($200) and uses very little power (can run >> off a 12v battery), and the toolchain and OS are all BSD-licensed (and >> everything will be published under that license). >> >> If someone is available for off-line discussion (to minimize unnecessary >> traffic to the list), I'd be more than willing to summarize the conversation >> and contribute it to the online documentation. >> >> Thank you, >> tim >> -- >> >> "Nuclear power is a hell of a way to boil water." -- Albert Einstein >> ___ >> users mailing list >> users@lists.open-mpi.org >> https://lists.open-mpi.org/mailman/listinfo/users > > ___ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users -- Jeff Squyres jsquy...@cisco.com ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
Re: [OMPI users] hwloc, OpenMPI and unsupported OSes and toolchains
My apologies for the duplicate posts. This was originally sent from my university email account. However, there was a configuration error at the mailing list host site that prevented email exchange between the host and my university, including confirmation that I had subscribed. Jeff Squyres manually subscribed me, and when a second send of this post did not go through, the mailing list host and my university's IT department figured it out. Once that was fixed these emails from my university account came through, after being held in queue. In the meantime I had switched to a different email account and sent the post. Gregory (tim) Kelly wrote: Hello Everyone, I'm inquiring to find someone that can answer some multi-part questions about hwloc, OpenMPI and an alternative OS and toolchain. I have a project as part of my PhD work, and it's not a simple, one-part question. For brevity, I am omitting details about the OS and toolchain, other than that neither are supported. If forced to choose between OpenMPI and the OS/toolchain, I am likely to choose the OS/toolchain and pursue other avenues for parallelization. That's part of what I am trying to determine with my inquiry, and not a reflection on OpenMPI. To summarize some of the question areas: 1) The OS I am working with does not support MP 2) nor does it support pthreads 3) the hardware is quad-core x86 SoC with an integrated memory controller 4) I'd like to see if it possible to utilize hwloc and shmem to build an asymmetric multi-processing system where only one core has I/O but the other three can run the executable This is a fairly dedicated system to be used for analyzing ODEs (disease models). The hardware is cheap ($200) and uses very little power (can run off a 12v battery), and the toolchain and OS are all BSD-licensed (and everything will be published under that license). If someone is available for off-line discussion (to minimize unnecessary traffic to the list), I'd be more than willing to summarize the conversation and contribute it to the online documentation. Thank you, tim -- "I don't want to be argumentative!" -- my then 11 year old son, in response to finding out his next writing assignment is an argumentative essay ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
Re: [OMPI users] hwloc, OpenMPI and unsupported OSes and toolchains
I don’t see how Open MPI can operate without pthreads > On Mar 19, 2018, at 3:23 PM, Gregory (tim) Kelly wrote: > > Hello Everyone, > I'm inquiring to find someone that can answer some multi-part questions about > hwloc, OpenMPI and an alternative OS and toolchain. I have a project as part > of my PhD work, and it's not a simple, one-part question. For brevity, I am > omitting details about the OS and toolchain, other than that neither are > supported. If forced to choose between OpenMPI and the OS/toolchain, I am > likely to choose the OS/toolchain and pursue other avenues for > parallelization. That's part of what I am trying to determine with my > inquiry. > > To summarize some of the question areas: > > 1) The OS I am working with does not support MP > 2) nor does it support pthreads > 3) the hardware is quad-core SoC with an integrated memory controller > 4) I'd like to see if it possible to utilize hwloc and shmem to build an > asymmetric multi-processing system where only one core has I/O but the other > three can run the executable > > This is a fairly dedicated system to be used for analyzing ODEs (disease > models). The hardware is cheap ($200) and uses very little power (can run > off a 12v battery), and the toolchain and OS are all BSD-licensed (and > everything will be published under that license). > > If someone is available for off-line discussion (to minimize unnecessary > traffic to the list), I'd be more than willing to summarize the conversation > and contribute it to the online documentation. > > Thank you, > tim > -- > > "Nuclear power is a hell of a way to boil water." -- Albert Einstein > ___ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
[OMPI users] hwloc, OpenMPI and unsupported OSes and toolchains
Hello Everyone, I'm inquiring to find someone that can answer some multi-part questions about hwloc, OpenMPI and an alternative OS and toolchain. I have a project as part of my PhD work, and it's not a simple, one-part question. For brevity, I am omitting details about the OS and toolchain, other than that neither are supported. If forced to choose between OpenMPI and the OS/toolchain, I am likely to choose the OS/toolchain and pursue other avenues for parallelization. That's part of what I am trying to determine with my inquiry, and not a reflection on OpenMPI. To summarize some of the question areas: 1) The OS I am working with does not support MP 2) nor does it support pthreads 3) the hardware is quad-core x86 SoC with an integrated memory controller 4) I'd like to see if it possible to utilize hwloc and shmem to build an asymmetric multi-processing system where only one core has I/O but the other three can run the executable This is a fairly dedicated system to be used for analyzing ODEs (disease models). The hardware is cheap ($200) and uses very little power (can run off a 12v battery), and the toolchain and OS are all BSD-licensed (and everything will be published under that license). If someone is available for off-line discussion (to minimize unnecessary traffic to the list), I'd be more than willing to summarize the conversation and contribute it to the online documentation. Thank you, tim -- "Nuclear power is a hell of a way to boil water." -- Albert Einstein ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
[OMPI users] hwloc, OpenMPI and unsupported OSes and toolchains
Hello Everyone, I'm inquiring to find someone that can answer some multi-part questions about hwloc, OpenMPI and an alternative OS and toolchain. I have a project as part of my PhD work, and it's not a simple, one-part question. For brevity, I am omitting details about the OS and toolchain, other than that neither are supported. If forced to choose between OpenMPI and the OS/toolchain, I am likely to choose the OS/toolchain and pursue other avenues for parallelization. That's part of what I am trying to determine with my inquiry. To summarize some of the question areas: 1) The OS I am working with does not support MP 2) nor does it support pthreads 3) the hardware is quad-core SoC with an integrated memory controller 4) I'd like to see if it possible to utilize hwloc and shmem to build an asymmetric multi-processing system where only one core has I/O but the other three can run the executable This is a fairly dedicated system to be used for analyzing ODEs (disease models). The hardware is cheap ($200) and uses very little power (can run off a 12v battery), and the toolchain and OS are all BSD-licensed (and everything will be published under that license). If someone is available for off-line discussion (to minimize unnecessary traffic to the list), I'd be more than willing to summarize the conversation and contribute it to the online documentation. Thank you, tim -- "Nuclear power is a hell of a way to boil water." -- Albert Einstein ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
Re: [OMPI users] hwloc, OpenMPI and unsupported OSes and toolchains
Hi Brice, Thank you for your response. Yes, possibly hardwiring everything would be easier. I was thinking I could use OpenMPI for the signaling between the cores on an OS that doesn't support multi-processing, using the shmem approach. The executable is the same for each CPU image, but the initial conditions will be different and have to be communicated from the master CPU, which will also be responsible for aggregating the results into a data and image file. Here's the hardware: https://shop.udoo.org/other/x86/udoo-x86-advanced-plus.html The OS running on CPU0 would have control of I/O and partition the memory. In testing to this point 1GB is sufficient to run the OS and executable. In fact, currently I do not free any memory so likely the footprint is much, much smaller. Not freeing the memory until execution is completed has avoided some malloc complaints. The OS does not have paging or segmentation, so fragmentation can be an issue. Performance is very good. Is is possible to use a shared memory approach and run an AMP set up, with hwloc? Would there be any benefit to doing so instead of the hardwiring approach you mention? tim Brice Goglin wrote: Hello I am available for off-line discussion for the hwloc side of things. But things look complicated here from your summary below. I guess there's no need for binding on such a system. And topology is quite simple, so it might be easier to hardwire everything. Brice Le 20/03/2018 à 08:36, Tim Kelly a écrit : Hello Everyone, I'm inquiring to find someone that can answer some multi-part questions about hwloc, OpenMPI and an alternative OS and toolchain. I have a project as part of my PhD work, and it's not a simple, one-part question. For brevity, I am omitting details about the OS and toolchain, other than that neither are supported. If forced to choose between OpenMPI and the OS/toolchain, I am likely to choose the OS/toolchain and pursue other avenues for parallelization. That's part of what I am trying to determine with my inquiry, and not a reflection on OpenMPI. To summarize some of the question areas: 1) The OS I am working with does not support MP 2) nor does it support pthreads 3) the hardware is quad-core x86 SoC with an integrated memory controller 4) I'd like to see if it possible to utilize hwloc and shmem to build an asymmetric multi-processing system where only one core has I/O but the other three can run the executable This is a fairly dedicated system to be used for analyzing ODEs (disease models). The hardware is cheap ($200) and uses very little power (can run off a 12v battery), and the toolchain and OS are all BSD-licensed (and everything will be published under that license). If someone is available for off-line discussion (to minimize unnecessary traffic to the list), I'd be more than willing to summarize the conversation and contribute it to the online documentation. Thank you, tim ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users -- Every chord has a key, every note a consequence ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
Re: [OMPI users] hwloc, OpenMPI and unsupported OSes and toolchains
Hello I am available for off-line discussion for the hwloc side of things. But things look complicated here from your summary below. I guess there's no need for binding on such a system. And topology is quite simple, so it might be easier to hardwire everything. Brice Le 20/03/2018 à 08:36, Tim Kelly a écrit : > Hello Everyone, > I'm inquiring to find someone that can answer some multi-part questions > about hwloc, OpenMPI and an alternative OS and toolchain. I have a > project as part of my PhD work, and it's not a simple, one-part > question. For brevity, I am omitting details about the OS and > toolchain, other than that neither are supported. If forced to choose > between OpenMPI and the OS/toolchain, I am likely to choose the > OS/toolchain and pursue other avenues for parallelization. That's part > of what I am trying to determine with my inquiry, and not a reflection > on OpenMPI. > > To summarize some of the question areas: > > 1) The OS I am working with does not support MP > 2) nor does it support pthreads > 3) the hardware is quad-core x86 SoC with an integrated memory controller > 4) I'd like to see if it possible to utilize hwloc and shmem to build an > asymmetric multi-processing system where only one core has I/O but the > other three can run the executable > > This is a fairly dedicated system to be used for analyzing ODEs (disease > models). The hardware is cheap ($200) and uses very little power (can > run off a 12v battery), and the toolchain and OS are all BSD-licensed > (and everything will be published under that license). > > If someone is available for off-line discussion (to minimize unnecessary > traffic to the list), I'd be more than willing to summarize the > conversation and contribute it to the online documentation. > > Thank you, > tim ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
[OMPI users] hwloc, OpenMPI and unsupported OSes and toolchains
Hello Everyone, I'm inquiring to find someone that can answer some multi-part questions about hwloc, OpenMPI and an alternative OS and toolchain. I have a project as part of my PhD work, and it's not a simple, one-part question. For brevity, I am omitting details about the OS and toolchain, other than that neither are supported. If forced to choose between OpenMPI and the OS/toolchain, I am likely to choose the OS/toolchain and pursue other avenues for parallelization. That's part of what I am trying to determine with my inquiry, and not a reflection on OpenMPI. To summarize some of the question areas: 1) The OS I am working with does not support MP 2) nor does it support pthreads 3) the hardware is quad-core x86 SoC with an integrated memory controller 4) I'd like to see if it possible to utilize hwloc and shmem to build an asymmetric multi-processing system where only one core has I/O but the other three can run the executable This is a fairly dedicated system to be used for analyzing ODEs (disease models). The hardware is cheap ($200) and uses very little power (can run off a 12v battery), and the toolchain and OS are all BSD-licensed (and everything will be published under that license). If someone is available for off-line discussion (to minimize unnecessary traffic to the list), I'd be more than willing to summarize the conversation and contribute it to the online documentation. Thank you, tim -- All we need is one more Mickey Mouse another golf course another country club another gated community -- JJ Grey ___ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
