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From: INTURU S. 2. <int...@vi...> - 2023-08-30 08:51:50
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Hello, I am building IBAMR open software as given in the link https://ibamr.github.io/. When I configured libmesh, I got the error mentioning "petsc was not found". I am sharing the config.log file. Please find the attachment and do the needful. Thanks and Regards Srinivas -- **Disclaimer:* This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of “Vellore Institute of Technology”. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* |
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From: INTURU S. 2. <int...@vi...> - 2023-08-30 10:49:11
Attachments:
libmesh.txt
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In continuation to the previous mail, I am sending the tasks done while configuring libmesh 1.6.2. The error is mentioned in this file. Please find the attached file and do the needful. Thanks and Regards Srinivas On Wed, Aug 30, 2023 at 1:47 PM INTURU SRINIVAS 20PHD0548 < int...@vi...> wrote: > Hello, > > I am building IBAMR open software as given in the link > https://ibamr.github.io/. When I configured libmesh, I got the error > mentioning "petsc was not found". I am sharing the config.log file. Please > find the attachment and do the needful. > > > Thanks and Regards > Srinivas > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of “Vellore Institute of Technology”. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* |
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From: John P. <jwp...@gm...> - 2023-08-30 20:26:22
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Hi, Is there a particular reason that you are trying to use libmesh 1.6.2? It's about two years old at this point, and there have been many updates and improvements (including a stable release) since that time, so you will probably have the most success if you use a more up-to-date version. The log you attached is the output of configure to the terminal, so it doesn't really give much information other than: <<< Could not find a viable PETSc Makefile to determine PETSC_CC_INCLUDES, etc. >>> You might be able to get more detailed info about the failure to find PETSc by looking at the config.log file generated by configure. -- John On Wed, Aug 30, 2023 at 5:49 AM INTURU SRINIVAS 20PHD0548 via Libmesh-users <lib...@li...> wrote: > In continuation to the previous mail, I am sending the tasks done while > configuring libmesh 1.6.2. The error is mentioned in this file. Please find > the attached file and do the needful. |
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From: INTURU S. 2. <int...@vi...> - 2023-08-31 03:50:14
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Hi John, IBAMR open software recommended libmesh 1.6.2. I sent a config.log file in the first email and this is from the libmesh directory. Is this the file you need? I am sending it again. Please find the attachment Thanks and regards Srinivas On Thu, Aug 31, 2023, 01:56 John Peterson <jwp...@gm...> wrote: > Hi, > > Is there a particular reason that you are trying to use libmesh 1.6.2? > It's about two years old at this point, and there have been many updates > and improvements (including a stable release) since that time, so you will > probably have the most success if you use a more up-to-date version. > > The log you attached is the output of configure to the terminal, so it > doesn't really give much information other than: > <<< Could not find a viable PETSc Makefile to determine PETSC_CC_INCLUDES, > etc. >>> > > You might be able to get more detailed info about the failure to find > PETSc by looking at the config.log file generated by configure. > > -- > John > > > On Wed, Aug 30, 2023 at 5:49 AM INTURU SRINIVAS 20PHD0548 via > Libmesh-users <lib...@li...> wrote: > >> In continuation to the previous mail, I am sending the tasks done while >> configuring libmesh 1.6.2. The error is mentioned in this file. Please >> find >> the attached file and do the needful. > > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of “Vellore Institute of Technology”. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* |
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From: John P. <jwp...@gm...> - 2023-08-31 14:28:40
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Hi,
The config.log that you sent this time does not seem to be related to the
previous one, but rather to a MOOSE build? And the version of PETSc is
totally different from the previous log, it is now PETSc 3.11.4.
In any event, the relevant configure output is:
configure:34458: checking for
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt//include/petscversion.h
> configure:34458: result: yes
> configure:34525: result: <<< Found PETSc 3.11.4 installation in
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt ... >>>
> configure:34535: checking whether we can compile a trivial PETSc program
> configure:34564: mpicxx -c -std=gnu++11
> -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include
> -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt//include
> -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include
> -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include conftest.cpp >&5
> In file included from
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscsys.h:14:0,
> from
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscbag.h:4,
> from
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petsc.h:5,
> from conftest.cpp:144:
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscconf.h:85:36:
> error: expected '}' before '__attribute'
> #define PETSC_DEPRECATED_ENUM(why) __attribute((deprecated))
> ^
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscksp.h:430:76:
> note: in expansion of macro 'PETSC_DEPRECATED_ENUM'
> #define KSP_DIVERGED_PCSETUP_FAILED_DEPRECATED
> KSP_DIVERGED_PCSETUP_FAILED PETSC_DEPRECATED_ENUM("Use
> KSP_DIVERGED_PC_FAILED (since v3.11)")
>
> ^
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscksp.h:452:15:
> note: in expansion of macro 'KSP_DIVERGED_PCSETUP_FAILED_DEPRECATED'
> KSP_DIVERGED_PCSETUP_FAILED_DEPRECATED = -11,
> ^
> In file included from
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscsnes.h:6:0,
> from
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscts.h:7,
> from
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petsc.h:29,
> from conftest.cpp:144:
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscksp.h:452:55:
> error: expected unqualified-id before '=' token
> KSP_DIVERGED_PCSETUP_FAILED_DEPRECATED = -11,
> ^
> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscksp.h:454:52:
> error: expected declaration before '}' token
> KSP_CONVERGED_ITERATING = 0} KSPConvergedReason;
> ^
So there is a syntax error related to the __attribute keyword that appears
in one of the PETSc header files. This means that the compiler you are
using:
configure:5255: mpicc --version >&5
> gcc (Homebrew GCC 5.5.0_7) 5.5.0
is also different from the one in your previous email, and is apparently
too old to be able to compile the version of PETSc you are using. Note that
PETSc 3.11.4 is from March 2019 while GCC 5.5 is from 2017, so this could
explain the discrepancy. These types of errors are pretty common when
trying to build old versions of software from source on newer (looks like
you are using Ubuntu 18.04) machines, so I would recommend using
contemporary versions of all software.
--
John
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From: INTURU S. 2. <int...@vi...> - 2023-08-31 15:43:52
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Sorry for the mistake. Please find the attached file.
On Thu, Aug 31, 2023 at 7:58 PM John Peterson <jwp...@gm...> wrote:
> Hi,
>
> The config.log that you sent this time does not seem to be related to the
> previous one, but rather to a MOOSE build? And the version of PETSc is
> totally different from the previous log, it is now PETSc 3.11.4.
>
> In any event, the relevant configure output is:
>
> configure:34458: checking for
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt//include/petscversion.h
>> configure:34458: result: yes
>> configure:34525: result: <<< Found PETSc 3.11.4 installation in
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt ... >>>
>> configure:34535: checking whether we can compile a trivial PETSc program
>> configure:34564: mpicxx -c -std=gnu++11
>> -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include
>> -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt//include
>> -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include
>> -I/opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include conftest.cpp >&5
>> In file included from
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscsys.h:14:0,
>> from
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscbag.h:4,
>> from
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petsc.h:5,
>> from conftest.cpp:144:
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscconf.h:85:36:
>> error: expected '}' before '__attribute'
>> #define PETSC_DEPRECATED_ENUM(why) __attribute((deprecated))
>> ^
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscksp.h:430:76:
>> note: in expansion of macro 'PETSC_DEPRECATED_ENUM'
>> #define KSP_DIVERGED_PCSETUP_FAILED_DEPRECATED
>> KSP_DIVERGED_PCSETUP_FAILED PETSC_DEPRECATED_ENUM("Use
>> KSP_DIVERGED_PC_FAILED (since v3.11)")
>>
>> ^
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscksp.h:452:15:
>> note: in expansion of macro 'KSP_DIVERGED_PCSETUP_FAILED_DEPRECATED'
>> KSP_DIVERGED_PCSETUP_FAILED_DEPRECATED = -11,
>> ^
>> In file included from
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscsnes.h:6:0,
>> from
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscts.h:7,
>> from
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petsc.h:29,
>> from conftest.cpp:144:
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscksp.h:452:55:
>> error: expected unqualified-id before '=' token
>> KSP_DIVERGED_PCSETUP_FAILED_DEPRECATED = -11,
>> ^
>> /opt/moose/petsc-3.11.4/mpich-3.3_gcc-9.2.0-opt/include/petscksp.h:454:52:
>> error: expected declaration before '}' token
>> KSP_CONVERGED_ITERATING = 0} KSPConvergedReason;
>> ^
>
>
> So there is a syntax error related to the __attribute keyword that appears
> in one of the PETSc header files. This means that the compiler you are
> using:
>
> configure:5255: mpicc --version >&5
>> gcc (Homebrew GCC 5.5.0_7) 5.5.0
>
>
>
> is also different from the one in your previous email, and is apparently
> too old to be able to compile the version of PETSc you are using. Note that
> PETSc 3.11.4 is from March 2019 while GCC 5.5 is from 2017, so this could
> explain the discrepancy. These types of errors are pretty common when
> trying to build old versions of software from source on newer (looks like
> you are using Ubuntu 18.04) machines, so I would recommend using
> contemporary versions of all software.
>
> --
> John
>
--
**Disclaimer:*
This message was sent from Vellore Institute of Technology.
The contents of this email may contain legally protected confidential or
privileged information of “Vellore Institute of Technology”. If you are
not the intended recipient, you should not disseminate, distribute or copy
this e-mail. Please notify the sender immediately and destroy all copies of
this message and any attachments. If you have received this email in error,
please promptly notify the sender by reply email and delete the original
email and any backup copies without reading them.*
|
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From: John P. <jwp...@gm...> - 2023-08-31 19:13:46
|
Unfortunately, there is no additional information in the log file beyond
configure:4977: result: <<< Could not find a viable PETSc Makefile to
> determine PETSC_CC_INCLUDES, etc. >>>
which means that your PETSc installation is not how we expected it to be.
Based on the args you passed to configure, I see that you set the following
PETSC_DIR=/home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug
PETSC_ARCH=linux-debug
In this case we expect to find the following two files:
${PETSC_DIR}/makefile
${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/variables
or the single file:
${PETSC_DIR}/lib/petsc/conf/variables
Therefore, I think the issue is that your PETSC_DIR variable already
includes the PETSC_ARCH in it? I would try again setting
PETSC_DIR=/home/hpcsmec15767/sfw/petsc/3.17.5
instead.
--
John
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From: INTURU S. 2. <int...@vi...> - 2023-09-01 06:26:02
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Hi John,
I tried with PETSC_DIR=/home/hpcsmec15767/sfw/petsc/3.17.5. I got the same
error as mentioned below
checking for built-in XDR support... yes
checking
/home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug/include/petscversion.h
usability... no
checking
/home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug/include/petscversion.h
presence... no
checking for
/home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug/include/petscversion.h... no
checking /home/hpcsmec15767/sfw/petsc/3.17.5/include/petscversion.h
usability... no
checking /home/hpcsmec15767/sfw/petsc/3.17.5/include/petscversion.h
presence... no
checking for /home/hpcsmec15767/sfw/petsc/3.17.5/include/petscversion.h...
no
configure: error: *** PETSc was not found, but --enable-petsc-required was
specified.
This one I am trying in the hpc cluster. Few months ago, I tried to install
this IBAMR-0.13.0 open software with petsc 3.17.5 and libmesh 1.6.2 in our
local machine, the same error occurred though.
Right now I am using IBAMR-0.11.0 with petsc 3.13.4 and libmesh 1.6.2 and
it is working in our local machine. Does petsc 3.17.5 version compatible
with libmesh 1.6.2?
I am sharing the config.log file. Please find the attachment and do the
needful.
Thanks and regards
Srinivas
On Fri, Sep 1, 2023 at 12:43 AM John Peterson <jwp...@gm...> wrote:
> Unfortunately, there is no additional information in the log file beyond
>
> configure:4977: result: <<< Could not find a viable PETSc Makefile to
>> determine PETSC_CC_INCLUDES, etc. >>>
>
>
> which means that your PETSc installation is not how we expected it to be.
> Based on the args you passed to configure, I see that you set the following
>
> PETSC_DIR=/home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug
> PETSC_ARCH=linux-debug
>
> In this case we expect to find the following two files:
> ${PETSC_DIR}/makefile
> ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/variables
>
> or the single file:
>
> ${PETSC_DIR}/lib/petsc/conf/variables
>
> Therefore, I think the issue is that your PETSC_DIR variable already
> includes the PETSC_ARCH in it? I would try again setting
>
> PETSC_DIR=/home/hpcsmec15767/sfw/petsc/3.17.5
>
> instead.
>
> --
> John
>
--
**Disclaimer:*
This message was sent from Vellore Institute of Technology.
The contents of this email may contain legally protected confidential or
privileged information of “Vellore Institute of Technology”. If you are
not the intended recipient, you should not disseminate, distribute or copy
this e-mail. Please notify the sender immediately and destroy all copies of
this message and any attachments. If you have received this email in error,
please promptly notify the sender by reply email and delete the original
email and any backup copies without reading them.*
|
|
From: John P. <jwp...@gm...> - 2023-09-01 14:52:36
|
On Fri, Sep 1, 2023 at 1:25 AM INTURU SRINIVAS 20PHD0548 < int...@vi...> wrote: > Hi John, > > I tried with PETSC_DIR=/home/hpcsmec15767/sfw/petsc/3.17.5. I got the > same error as mentioned below > checking for built-in XDR support... yes > checking > /home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug/include/petscversion.h > usability... no > checking > /home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug/include/petscversion.h > presence... no > checking for > /home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug/include/petscversion.h... no > checking /home/hpcsmec15767/sfw/petsc/3.17.5/include/petscversion.h > usability... no > checking /home/hpcsmec15767/sfw/petsc/3.17.5/include/petscversion.h > presence... no > checking for /home/hpcsmec15767/sfw/petsc/3.17.5/include/petscversion.h... > no > configure: error: *** PETSc was not found, but --enable-petsc-required was > specified. > > This one I am trying in the hpc cluster. Few months ago, I tried to > install this IBAMR-0.13.0 open software with petsc 3.17.5 and libmesh 1.6.2 > in our local machine, the same error occurred though. > Right now I am using IBAMR-0.11.0 with petsc 3.13.4 and libmesh 1.6.2 and > it is working in our local machine. > Does petsc 3.17.5 version compatible with libmesh 1.6.2? > The PETSc 3.17.x release series was started in March 2022 commit 30c35bf2dfad782abeabcf00da45fe2af1c737cf (tag: v3.17.0) > Author: Satish Balay <ba...@mc...> > Date: Wed Mar 30 20:50:56 2022 -0500 While libmesh 1.6.2 is from August 2021: commit e98f7419bd062d4c6b3cc3727899e892915af730 (tag: v1.6.2) > Author: John W. Peterson <jwp...@gm...> > Date: Mon Aug 2 14:59:29 2021 -0500 so it predates PETSc 3.17 by several months. Therefore it's definitely possible they are not compatible. Out of curiosity, where is petscversion.h actually located in your installation of PETSc, since it is not located in any of the places listed above? Also, how exactly do you install PETSc? If you follow the directions that are printed to the screen when building PETSc from source then the PETSc headers should just be located at $PETSC_DIR/include and $PETSC_ARCH is not needed/used by libmesh configure. -- John |
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From: INTURU S. 2. <int...@vi...> - 2023-09-03 07:16:36
|
Hi John, With the information you gave, I tried to install the latest libmesh version 1.7.1 and it was successful. Thanks for your valuable suggestions and the support. With regards Srinivas On Fri, Sep 1, 2023 at 8:22 PM John Peterson <jwp...@gm...> wrote: > > > On Fri, Sep 1, 2023 at 1:25 AM INTURU SRINIVAS 20PHD0548 < > int...@vi...> wrote: > >> Hi John, >> >> I tried with PETSC_DIR=/home/hpcsmec15767/sfw/petsc/3.17.5. I got the >> same error as mentioned below >> checking for built-in XDR support... yes >> checking >> /home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug/include/petscversion.h >> usability... no >> checking >> /home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug/include/petscversion.h >> presence... no >> checking for >> /home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug/include/petscversion.h... no >> checking /home/hpcsmec15767/sfw/petsc/3.17.5/include/petscversion.h >> usability... no >> checking /home/hpcsmec15767/sfw/petsc/3.17.5/include/petscversion.h >> presence... no >> checking for >> /home/hpcsmec15767/sfw/petsc/3.17.5/include/petscversion.h... no >> configure: error: *** PETSc was not found, but --enable-petsc-required >> was specified. >> >> This one I am trying in the hpc cluster. Few months ago, I tried to >> install this IBAMR-0.13.0 open software with petsc 3.17.5 and libmesh 1.6.2 >> in our local machine, the same error occurred though. >> Right now I am using IBAMR-0.11.0 with petsc 3.13.4 and libmesh 1.6.2 and >> it is working in our local machine. >> > > > Does petsc 3.17.5 version compatible with libmesh 1.6.2? >> > > The PETSc 3.17.x release series was started in March 2022 > > commit 30c35bf2dfad782abeabcf00da45fe2af1c737cf (tag: v3.17.0) >> Author: Satish Balay <ba...@mc...> >> Date: Wed Mar 30 20:50:56 2022 -0500 > > > While libmesh 1.6.2 is from August 2021: > > commit e98f7419bd062d4c6b3cc3727899e892915af730 (tag: v1.6.2) >> Author: John W. Peterson <jwp...@gm...> >> Date: Mon Aug 2 14:59:29 2021 -0500 > > > so it predates PETSc 3.17 by several months. Therefore it's definitely > possible they are not compatible. Out of curiosity, where is petscversion.h > actually located in your installation of PETSc, since it is not located in > any of the places listed above? Also, how exactly do you install PETSc? If > you follow the directions that are printed to the screen when building > PETSc from source then the PETSc headers should just be located at > $PETSC_DIR/include and $PETSC_ARCH is not needed/used by libmesh configure. > > -- > John > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of “Vellore Institute of Technology”. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* |
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