Re: [NMusers] Microsoft MPI

From: Ruben Faelens <ruben.faelens_at_gmail.com>
Date: Tue, 16 Apr 2019 20:17:57 +0200

Hi Mark,

See
https://wiki.mpich.org/mpich/index.php/Frequently_Asked_Questions#Q:_Why_can.27t_I_build_MPICH_on_Windows_anymore.3F

"We recommend all Windows users migrate to using MS-MPI."
There are many security risks with keeping MPICH2 around.

Please provide some more information. The NMFE script both compiles a
NONMEM executable and executes it.
1) Does compilation work? Are you definitely linking to the MS-MPI library?
Can you verify this with an object inspector?
2) What happens if you run nonmem in MPI mode without the required mpiexec
wrapper? Is there an error message from MS-MPI? What happens if you do run
it with mpiexec? Does the provided example MS-MPI fortran code work
independently of NONMEM?

/ Ruben

On Tue, Apr 16, 2019 at 8:05 PM Mark Sale <msale_at_nuventra.com> wrote:

> Thanks Ruben,
>
> I'll give it a try, but I think I did those things. Not sure that
> mpich2 is outdated- it works just fine, but isn't compatible with Rmpi
> package, and it seems I can't have both on a machine, need to "pick a side"
> (Microsoft or non-Microsoft). Not clear there is a way to specify which
> mpiexec to use in a given application, along with lots of other stuff I
> don't understand.
>
>
>
>
>
>
>
> Mark Sale M.D.
>
> Senior Vice President, Pharmacometrics
>
> Nuventra Pharma Sciences, Inc.
> 2525 Meridian Parkway, Suite 200
> Durham, NC 27713
>
> Phone (919)-973-0383
>
> msale_at_nuventra.com <http://msale_at_kinetigen.com>
>
>
>
> *Join Nuventra at upcoming events:*
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> CONFIDENTIALITY NOTICE The information in this transmittal (including
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> ------------------------------
> *From:* Ruben Faelens <ruben.faelens_at_gmail.com>
> *Sent:* Tuesday, April 16, 2019 10:58:45 AM
> *To:* Mark Sale
> *Cc:* nmusers_at_globomaxnm.com
> *Subject:* Re: [NMusers] Microsoft MPI
>
>
> *WARNING*: This email originated from outside of the company. *Do not
> click links or open* attachments unless you recognize the sender and are
> expecting the message.
> Hi Mark,
>
> Last time I tried this (2016, Windows 8 64-bit), NONMEM needed some
> convincing:
> 1) You have to copy over the right object files from Microsoft MPI into
> the NONMEM mpi link directory mpi\mpi_wini; _and_ change the nmfe compiler
> call to include the right Microsoft MPI libraries. This should allow you to
> compile a nonmem executable using the Microsoft MPI libraries.
> 2) You need to launch nonmem with the right wrapper (I think it was
> mpiexec)
> 3) You have to configure firewall rules to allow local communication for
> MPI. This may be tricky, as windows detects each nonmem.exe as a different
> executable with different firewall rules. If I remember correctly, this is
> where I got stuck last time.
> It *did* work however when deactivating the Windows Firewall.
>
> Hopefully these vague pointers can help you; I unfortunately did not
> retain my notes.
> If you get it working, it would be worthwhile to document this process for
> the community! My suggestions to link to Microsoft MPI by default (as
> mpich2 is hopelessly outdates) were not high on ICON's priority list.
>
> Best regards,
> Ruben
>
> On Tue, Apr 16, 2019 at 5:50 PM Mark Sale <msale_at_nuventra.com> wrote:
>
> Does anyone have any experience getting parallel NONMEM to run with the
> latest Microsoft MPI (version 10)?
>
> https://docs.microsoft.com/en-us/message-passing-interface/microsoft-mpi
> Microsoft MPI - Message Passing Interface | Microsoft Docs
> <https://docs.microsoft.com/en-us/message-passing-interface/microsoft-mpi>
> docs.microsoft.com
> Microsoft MPI. 03/28/2018; 2 minutes to read; Contributors. In this
> article. Microsoft MPI (MS-MPI) is a Microsoft implementation of the
> Message Passing Interface standard for developing and running parallel
> applications on the Windows platform.. MS-MPI offers several benefits:
>
>
>
> we need to run this for another parallel application, and when we
> installed it, it broke parallel NONMEM. We're using Intel Fortran, 64 bit
> Window Server (2012).
>
>
> thanks
>
>
>
> Mark Sale M.D.
>
> Senior Vice President, Pharmacometrics
>
> Nuventra Pharma Sciences, Inc.
> 2525 Meridian Parkway, Suite 200
> Durham, NC 27713
>
> Phone (919)-973-0383
>
> msale_at_nuventra.com <http://msale_at_kinetigen.com>
>
>
>
> *Join Nuventra at upcoming events:*
>
> AAPS <https://www.nuventra.com/resources/events/aaps-pharmsci-360/> |
> November 4-7 | Washington, DC | Booth #701
>
> The Path to IND
> <https://www.nuventra.com/resources/events/webinar-the-path-to-ind/> |
> Webinar | November 14 | 1pm-2pm
>
>
>
> *Check out our latest* blog post
> <https://www.nuventra.com/resources/blog/>*.*
>
>
> CONFIDENTIALITY NOTICE The information in this transmittal (including
> attachments, if any) may be privileged and confidential and is intended
> only for the recipient(s) listed above. Any review, use, disclosure,
> distribution or copying of this transmittal, in any form, is prohibited
> except by or on behalf of the intended recipient(s). If you have received
> this transmittal in error, please notify me immediately by reply email and
> destroy all copies of the transmittal.
>
>


Received on Tue Apr 16 2019 - 14:17:57 EDT

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