<div dir="ltr"><br><div class="gmail_extra">Hi Wesley,<br></div><div class="gmail_extra"><br></div><div class="gmail_extra">How could I do that? as I read in the internet. I have to set:<br></div><div class="gmail_extra"> include "mpif.h"<br>
</div><div class="gmail_extra"> Call MPI_COMM_FREE<br><br></div><div class="gmail_extra">I found where I can set that in FLASH code ( I have attached the file) So I set:<br> integer, parameter :: FLASH_COMM = MPI_COMM_FREE<br>
</div><div class="gmail_extra">but I got an error when I compile the code:<br><br> Included at Driver_abortFlash.F90:34:<br><br> integer, parameter :: FLASH_COMM = MPI_COMM_FREE<br> 1<br>
Error: Symbol 'flash_comm' at (1) already has basic type of INTEGER<br>make: *** [Driver_abortFlash.o] Error 1<br><br></div><div class="gmail_extra">the code used MPI_COMM_WORLD.<br></div><div class="gmail_extra">
So is there a way to fix that?<br><br></div><div class="gmail_extra">Thanks,<br></div><div class="gmail_extra">Reem<br></div><div class="gmail_extra"><br></div><div class="gmail_extra"><br><div class="gmail_quote"><br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Date: Mon, 8 Jul 2013 10:25:38 -0500<br>
From: Wesley Bland <<a href="mailto:wbland@mcs.anl.gov">wbland@mcs.anl.gov</a>><br>
To: <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
Subject: Re: [mpich-discuss] discuss Digest, Vol 9, Issue 13<br>
Message-ID: <<a href="mailto:9A8EEBB2-72BB-429B-9368-150983B1C283@mcs.anl.gov">9A8EEBB2-72BB-429B-9368-150983B1C283@mcs.anl.gov</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
That's the correct way to set that environment variable, but I would have to agree with Pavan here. If you're running into the cap on context id's (especially with so few processes) it would seem that you're creating a lot of communicators that you probably don't need. Are you sure that you're freeing them correctly after use?<br>
<br>
Wesley<br>
<br>
On Jul 8, 2013, at 10:05 AM, Reem Alraddadi <<a href="mailto:raba500@york.ac.uk">raba500@york.ac.uk</a>> wrote:<br>
<br>
> Hi Wesley.<br>
> I wrote the following:<br>
> mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4<br>
> but the error still the same. Did I do it in the wrong way??<br>
><br>
> Thanks,<br>
> Reem<br>
><br>
> Message: 5<br>
> Date: Mon, 8 Jul 2013 08:14:48 -0500<br>
> From: Wesley Bland <<a href="mailto:wbland@mcs.anl.gov">wbland@mcs.anl.gov</a>><br>
> To: <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
> Subject: Re: [mpich-discuss] mpich on Mac os x<br>
> Message-ID: <<a href="mailto:8DC984B2-4E4B-4BFE-806E-203463A7A4E4@mcs.anl.gov">8DC984B2-4E4B-4BFE-806E-203463A7A4E4@mcs.anl.gov</a>><br>
> Content-Type: text/plain; charset=iso-8859-1<br>
><br>
> It seems that you're creating more communicators than MPICH can handle. It's possible that you might be able to get around this by setting the environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller than its default (which is 2). That frees up a few more communicators, but there is a pathological case where even with fewer communicators than the max, MPICH won't be able to agree on a new communicator id when needed. Try changing that environment variable and see if that fixes things.<br>
><br>
> Wesley<br>
><br>
> On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <<a href="mailto:raba500@york.ac.uk">raba500@york.ac.uk</a>> wrote:<br>
><br>
> > Hi all,<br>
> > I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. It works fine in the beginning of the run and then I got the following error:<br>
> ><br>
> > Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> > MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002, group=0xc8001349, new_comm=0x7fff606a8614) failed<br>
> > MPI_Comm_create(577).................:<br>
> > MPIR_Comm_create_intra(241)..........:<br>
> > MPIR_Get_contextid(799)..............:<br>
> > MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID because of fragmentation (169/2048 free on this process; ignore_id=0)<br>
> > Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> > MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002, group=0xc80012b6, new_comm=0x7fff670cc614) failed<br>
> > MPI_Comm_create(577).................:<br>
> > MPIR_Comm_create_intra(241)..........:<br>
> > MPIR_Get_contextid(799)..............:<br>
> > MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID because of fragmentation (316/2048 free on this process; ignore_id=0)<br>
> > Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> > MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000004, group=0xc800000e, new_comm=0x7fff629d5614) failed<br>
> > MPI_Comm_create(577).................:<br>
> > MPIR_Comm_create_intra(241)..........:<br>
> > MPIR_Get_contextid(799)..............:<br>
> > MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID because of fragmentation (2020/2048 free on this process; ignore_id=0)<br>
> > Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> > MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002, group=0xc8000020, new_comm=0x7fff639ae614) failed<br>
> > MPI_Comm_create(577).................:<br>
> > MPIR_Comm_create_intra(241)..........:<br>
> > MPIR_Get_contextid(799)..............:<br>
> > MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID because of fragmentation (2002/2048 free on this process; ignore_id=0<br>
> ><br>
> > Is there a way to fix that ?<br>
> ><br>
> > Thanks,<br>
> > Reem<br></blockquote><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
On Mon, Jul 8, 2013 at 9:17 AM, Pavan Balaji <<a href="mailto:balaji@mcs.anl.gov">balaji@mcs.anl.gov</a>> wrote:<br>
><br>
> Also make sure you are freeing unused communicators.<br>
><br>
> -- Pavan<br>
><br>
> On 07/08/2013 08:14 AM, Wesley Bland wrote:<br>
>><br>
>> It seems that you're creating more communicators than MPICH can handle.<br>
>> It's possible that you might be able to get around this by setting the<br>
>> environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller than<br>
>> its default (which is 2). That frees up a few more communicators, but there<br>
>> is a pathological case where even with fewer communicators than the max,<br>
>> MPICH won't be able to agree on a new communicator id when needed. Try<br>
>> changing that environment variable and see if that fixes things.<br>
>><br>
>> Wesley<br>
>><br>
>> On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <<a href="mailto:raba500@york.ac.uk">raba500@york.ac.uk</a>> wrote:<br>
>><br>
>>> Hi all,<br>
>>> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. It<br>
>>> works fine in the beginning of the run and then I got the following error:<br>
>>><br>
>>> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
>>> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002,<br>
>>> group=0xc8001349, new_comm=0x7fff606a8614) failed<br>
>>> MPI_Comm_create(577).................:<br>
>>> MPIR_Comm_create_intra(241)..........:<br>
>>> MPIR_Get_contextid(799)..............:<br>
>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID<br>
>>> because of fragmentation (169/2048 free on this process; ignore_id=0)<br>
>>> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
>>> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002,<br>
>>> group=0xc80012b6, new_comm=0x7fff670cc614) failed<br>
>>> MPI_Comm_create(577).................:<br>
>>> MPIR_Comm_create_intra(241)..........:<br>
>>> MPIR_Get_contextid(799)..............:<br>
>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID<br>
>>> because of fragmentation (316/2048 free on this process; ignore_id=0)<br>
>>> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
>>> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000004,<br>
>>> group=0xc800000e, new_comm=0x7fff629d5614) failed<br>
>>> MPI_Comm_create(577).................:<br>
>>> MPIR_Comm_create_intra(241)..........:<br>
>>> MPIR_Get_contextid(799)..............:<br>
>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID<br>
>>> because of fragmentation (2020/2048 free on this process; ignore_id=0)<br>
>>> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
>>> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002,<br>
>>> group=0xc8000020, new_comm=0x7fff639ae614) failed<br>
>>> MPI_Comm_create(577).................:<br>
>>> MPIR_Comm_create_intra(241)..........:<br>
>>> MPIR_Get_contextid(799)..............:<br>
>>> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID<br>
>>> because of fragmentation (2002/2048 free on this process; ignore_id=0<br>
>>><br>
>>> Is there a way to fix that ?<br>
>>><br>
>>> Thanks,<br>
>>> Reem<br>
>>> _______________________________________________<br>
>>> discuss mailing list <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
>>> To manage subscription options or unsubscribe:<br>
>>> <a href="https://lists.mpich.org/mailman/listinfo/discuss" target="_blank">https://lists.mpich.org/mailman/listinfo/discuss</a><br>
>><br>
>><br>
>> _______________________________________________<br>
>> discuss mailing list <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
>> To manage subscription options or unsubscribe:<br>
>> <a href="https://lists.mpich.org/mailman/listinfo/discuss" target="_blank">https://lists.mpich.org/mailman/listinfo/discuss</a><br>
>><br>
><br>
> --<br>
> Pavan Balaji<br>
> <a href="http://www.mcs.anl.gov/~balaji" target="_blank">http://www.mcs.anl.gov/~balaji</a><br>
> _______________________________________________<br>
> discuss mailing list <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
> To manage subscription options or unsubscribe:<br>
> <a href="https://lists.mpich.org/mailman/listinfo/discuss" target="_blank">https://lists.mpich.org/mailman/listinfo/discuss</a><br>
<br>
<br>
<br>
--<br>
Jeff Hammond<br>
<a href="mailto:jeff.science@gmail.com">jeff.science@gmail.com</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Mon, 8 Jul 2013 16:39:03 +0100<br>
From: Reem Alraddadi <<a href="mailto:raba500@york.ac.uk">raba500@york.ac.uk</a>><br>
To: <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
Subject: [mpich-discuss] mpich on Mac os x<br>
Message-ID:<br>
<<a href="mailto:CANKsntEJR0b_TA-tbdBO3fOV2O8PkwTG82a718qZPd3FnEBT3w@mail.gmail.com">CANKsntEJR0b_TA-tbdBO3fOV2O8PkwTG82a718qZPd3FnEBT3w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Pavan,<br>
<br>
Could you explain more what do you mean by that? I am sorry I am still<br>
beginner in MPICH.<br>
<br>
Hi Wesley,<br>
apologize about my first confused reply I have forgotten to change the<br>
subject. However, as I mentioned I wrote the following line:<br>
<br>
mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4<br>
<br>
I am wondering if I made any mistake here as the problem is still the same<br>
<br>
Thanks,<br>
Reem<br>
<br>
<br>
<br>
Message: 1<br>
> Date: Mon, 08 Jul 2013 09:17:00 -0500<br>
> From: Pavan Balaji <<a href="mailto:balaji@mcs.anl.gov">balaji@mcs.anl.gov</a>><br>
> To: <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
> Subject: Re: [mpich-discuss] mpich on Mac os x<br>
> Message-ID: <<a href="mailto:51DAC9DC.5000502@mcs.anl.gov">51DAC9DC.5000502@mcs.anl.gov</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
><br>
> Also make sure you are freeing unused communicators.<br>
><br>
> -- Pavan<br>
><br>
> On 07/08/2013 08:14 AM, Wesley Bland wrote:<br>
> > It seems that you're creating more communicators than MPICH can handle.<br>
> It's possible that you might be able to get around this by setting the<br>
> environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller than<br>
> its default (which is 2). That frees up a few more communicators, but there<br>
> is a pathological case where even with fewer communicators than the max,<br>
> MPICH won't be able to agree on a new communicator id when needed. Try<br>
> changing that environment variable and see if that fixes things.<br>
> ><br>
> > Wesley<br>
> ><br>
> > On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <<a href="mailto:raba500@york.ac.uk">raba500@york.ac.uk</a>> wrote:<br>
> ><br>
> >> Hi all,<br>
> >> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. It<br>
> works fine in the beginning of the run and then I got the following error:<br>
> >><br>
> >> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> >> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002,<br>
> group=0xc8001349, new_comm=0x7fff606a8614) failed<br>
> >> MPI_Comm_create(577).................:<br>
> >> MPIR_Comm_create_intra(241)..........:<br>
> >> MPIR_Get_contextid(799)..............:<br>
> >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID<br>
> because of fragmentation (169/2048 free on this process; ignore_id=0)<br>
> >> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> >> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002,<br>
> group=0xc80012b6, new_comm=0x7fff670cc614) failed<br>
> >> MPI_Comm_create(577).................:<br>
> >> MPIR_Comm_create_intra(241)..........:<br>
> >> MPIR_Get_contextid(799)..............:<br>
> >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID<br>
> because of fragmentation (316/2048 free on this process; ignore_id=0)<br>
> >> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> >> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000004,<br>
> group=0xc800000e, new_comm=0x7fff629d5614) failed<br>
> >> MPI_Comm_create(577).................:<br>
> >> MPIR_Comm_create_intra(241)..........:<br>
> >> MPIR_Get_contextid(799)..............:<br>
> >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID<br>
> because of fragmentation (2020/2048 free on this process; ignore_id=0)<br>
> >> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> >> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002,<br>
> group=0xc8000020, new_comm=0x7fff639ae614) failed<br>
> >> MPI_Comm_create(577).................:<br>
> >> MPIR_Comm_create_intra(241)..........:<br>
> >> MPIR_Get_contextid(799)..............:<br>
> >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID<br>
> because of fragmentation (2002/2048 free on this process; ignore_id=0<br>
> >><br>
> >> Is there a way to fix that ?<br>
> >><br>
> >> Thanks,<br>
> >> Reem<br>
> >> _______________________________________________<br>
> >> discuss mailing list <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
> >> To manage subscription options or unsubscribe:<br>
> >> <a href="https://lists.mpich.org/mailman/listinfo/discuss" target="_blank">https://lists.mpich.org/mailman/listinfo/discuss</a><br>
> ><br>
> > _______________________________________________<br>
> > discuss mailing list <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
> > To manage subscription options or unsubscribe:<br>
> > <a href="https://lists.mpich.org/mailman/listinfo/discuss" target="_blank">https://lists.mpich.org/mailman/listinfo/discuss</a><br>
> ><br>
><br>
> --<br>
> Pavan Balaji<br>
> <a href="http://www.mcs.anl.gov/~balaji" target="_blank">http://www.mcs.anl.gov/~balaji</a><br>
><br>
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------------------------------<br>
<br>
Message: 4<br>
Date: Mon, 8 Jul 2013 10:53:48 -0500<br>
From: Wesley Bland <<a href="mailto:wbland@mcs.anl.gov">wbland@mcs.anl.gov</a>><br>
To: <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
Subject: Re: [mpich-discuss] mpich on Mac os x<br>
Message-ID: <<a href="mailto:CEEC8B51-FFDF-40FE-BE56-E25F9C05BB27@mcs.anl.gov">CEEC8B51-FFDF-40FE-BE56-E25F9C05BB27@mcs.anl.gov</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On Jul 8, 2013, at 10:39 AM, Reem Alraddadi <<a href="mailto:raba500@york.ac.uk">raba500@york.ac.uk</a>> wrote:<br>
<br>
> Hi Pavan,<br>
><br>
> Could you explain more what do you mean by that? I am sorry I am still beginner in MPICH.<br>
<br>
This isn't specific to MPICH. This would be the case with any MPI implementation. What he means is that you need to make sure that when you are done using a communicator, you call MPI_Comm_free(communicator) so MPICH can free the internal resources used by the communicator. If you never free your communicators, then you will eventually run out. There is a limited number of communicators available internally.<br>
<br>
><br>
> Hi Wesley,<br>
> apologize about my first confused reply I have forgotten to change the subject. However, as I mentioned I wrote the following line:<br>
><br>
> mpirun --np 4 --env MPIR_PARAM_CTXID_EAGER_SIZE 1 ./flash4<br>
><br>
> I am wondering if I made any mistake here as the problem is still the same<br>
<br>
Yes, that's the correct way to use it, so that means your problem is probably what we described above.<br>
<br>
><br>
> Thanks,<br>
> Reem<br>
><br>
><br>
><br>
> Message: 1<br>
> Date: Mon, 08 Jul 2013 09:17:00 -0500<br>
> From: Pavan Balaji <<a href="mailto:balaji@mcs.anl.gov">balaji@mcs.anl.gov</a>><br>
> To: <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
> Subject: Re: [mpich-discuss] mpich on Mac os x<br>
> Message-ID: <<a href="mailto:51DAC9DC.5000502@mcs.anl.gov">51DAC9DC.5000502@mcs.anl.gov</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
><br>
> Also make sure you are freeing unused communicators.<br>
><br>
> -- Pavan<br>
><br>
> On 07/08/2013 08:14 AM, Wesley Bland wrote:<br>
> > It seems that you're creating more communicators than MPICH can handle. It's possible that you might be able to get around this by setting the environment variable MPIR_PARAM_CTXID_EAGER_SIZE to something smaller than its default (which is 2). That frees up a few more communicators, but there is a pathological case where even with fewer communicators than the max, MPICH won't be able to agree on a new communicator id when needed. Try changing that environment variable and see if that fixes things.<br>
> ><br>
> > Wesley<br>
> ><br>
> > On Jul 8, 2013, at 5:33 AM, Reem Alraddadi <<a href="mailto:raba500@york.ac.uk">raba500@york.ac.uk</a>> wrote:<br>
> ><br>
> >> Hi all,<br>
> >> I am using mpich-3.0.4 on Mac os x version 10.7.5 to run FLASH code. It works fine in the beginning of the run and then I got the following error:<br>
> >><br>
> >> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> >> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002, group=0xc8001349, new_comm=0x7fff606a8614) failed<br>
> >> MPI_Comm_create(577).................:<br>
> >> MPIR_Comm_create_intra(241)..........:<br>
> >> MPIR_Get_contextid(799)..............:<br>
> >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID because of fragmentation (169/2048 free on this process; ignore_id=0)<br>
> >> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> >> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002, group=0xc80012b6, new_comm=0x7fff670cc614) failed<br>
> >> MPI_Comm_create(577).................:<br>
> >> MPIR_Comm_create_intra(241)..........:<br>
> >> MPIR_Get_contextid(799)..............:<br>
> >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID because of fragmentation (316/2048 free on this process; ignore_id=0)<br>
> >> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> >> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000004, group=0xc800000e, new_comm=0x7fff629d5614) failed<br>
> >> MPI_Comm_create(577).................:<br>
> >> MPIR_Comm_create_intra(241)..........:<br>
> >> MPIR_Get_contextid(799)..............:<br>
> >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID because of fragmentation (2020/2048 free on this process; ignore_id=0)<br>
> >> Fatal error in MPI_Comm_create: Other MPI error, error stack:<br>
> >> MPI_Comm_create(600).................: MPI_Comm_create(comm=0x84000002, group=0xc8000020, new_comm=0x7fff639ae614) failed<br>
> >> MPI_Comm_create(577).................:<br>
> >> MPIR_Comm_create_intra(241)..........:<br>
> >> MPIR_Get_contextid(799)..............:<br>
> >> MPIR_Get_contextid_sparse_group(1146): Cannot allocate context ID because of fragmentation (2002/2048 free on this process; ignore_id=0<br>
> >><br>
> >> Is there a way to fix that ?<br>
> >><br>
> >> Thanks,<br>
> >> Reem<br>
> >> _______________________________________________<br>
> >> discuss mailing list <a href="mailto:discuss@mpich.org">discuss@mpich.org</a><br>
> >> To manage subscription options or unsubscribe:<br>
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