Re: [deal.II] University cluster installation issue: compilers

[Stephanie Sparks]

I was able to install p4est successfully by 

(1) setting CFLAGS="-std=c99"
(2) editing the sc_io.c file per the suggestion on the github issue page 
opened by Wolfgang
(3) defining the mathematical constants (specifically M_PI, M_PI_4, and 
M_SQRT2) in each script that used one (a partial list was added to the 
github issue for this).

Since the install worked I didn't try the older version.

Thanks all!

On Wednesday, March 9, 2022 at 1:24:09 PM UTC-7 Stephanie Sparks wrote:

> Hi Timo,
>
> I get the following: 
>
> icc version 19.0.4.243 (gcc version 4.8.5 compatibility)
>
> I'll try with an older version of p4est now.
>
> Stephanie
>
> On Wednesday, March 9, 2022 at 10:31:51 AM UTC-7 Timo Heister wrote:
>
>> Stephanie,
>>
>> What does "icc -v" return for you? I can compile p4est 2.3.2 with icc
>> version 19.1.1.217
>>
>> You can also try an older p4est release like 2.2 instead of having to
>> fix a bunch of bugs inside the codebase.
>>
>>
>>
>>
>> On Mon, Mar 7, 2022 at 2:57 PM Wolfgang Bangerth  
>> wrote:
>> >
>> > On 3/7/22 12:22, Stephanie Sparks wrote:
>> > >
>> > > The #include  declaration did not seem to work; however, as I
>> > > still get the same error.
>> > >
>> > > Should I note this on the github issue?
>> >
>> > Yes, please do.
>> >
>> > You can just put
>> > #define M_PI 3.14159265358979323846264338327950288
>> > anywhere in that file (before the first place where it is used) then.
>> >
>> > Best
>> > W.
>> >
>> > --
>> > 
>> > Wolfgang Bangerth email: bang...@colostate.edu
>> > www: http://www.math.colostate.edu/~bangerth/
>> >
>> > --
>> > The deal.II project is located at http://www.dealii.org/
>> > For mailing list/forum options, see 
>> https://groups.google.com/d/forum/dealii?hl=en
>> > ---
>> > You received this message because you are subscribed to the Google 
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>> https://groups.google.com/d/msgid/dealii/4892fe8a-1693-acb4-cb6d-7e62af782377%40colostate.edu
>> .
>>
>>
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>>
>

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Re: [deal.II] University cluster installation issue: compilers

[Stephanie Sparks]

Thank you Wolfgang!

I added #include  to the sc_io.c file and that fixed the error I 
was getting for that one.

The #include  declaration did not seem to work; however, as I still 
get the same error.

Should I note this on the github issue?

Thanks,
Stephanie

On Monday, March 7, 2022 at 7:54:42 AM UTC-7 Wolfgang Bangerth wrote:

> On 3/4/22 16:51, Stephanie Sparks wrote:
> > 
> > I did try to specify C99 as you suggested 
>
> OK, good news that that worked at least.
>
>
> >but I get a new error now:
> > 
> > /home/saspark2/build2//tmp/unpack/p4est-2.3.2/sc/src/sc_io.c(581): 
> warning 
> > #266: function "fileno" declared implicitly
> > retval = fsync (fileno (file));
> > ^
> > 
> > /home/saspark2/build2//tmp/unpack/p4est-2.3.2/sc/src/sc_random.c(153): 
> error: 
> > identifier "M_PI" is undefined
> > t = tan (M_PI * sc_rand (state));
> >  ^
>
> I'm afraid that you might have to edit these source files yourself. We're 
> not 
> the authors of p4est, so there is nothing I can fix myself, but I did open 
> github issues for everything:
> https://github.com/cburstedde/libsc/issues/66
> https://github.com/cburstedde/libsc/issues/65
> https://github.com/cburstedde/p4est/issues/133
> I *think* that it should work if you added the #include directives 
> mentioned 
> in these issues to the two libsc files. This may or may not be enough to 
> get 
> things compiled...
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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Re: [deal.II] University cluster installation issue: compilers

[Stephanie Sparks]

Thanks Wolfgang for that suggestion.

I did try to specify C99 as you suggested but I get a new error now:

/home/saspark2/build2//tmp/unpack/p4est-2.3.2/sc/src/sc_io.c(581): warning 
#266: function "fileno" declared implicitly
retval = fsync (fileno (file));
^

/home/saspark2/build2//tmp/unpack/p4est-2.3.2/sc/src/sc_random.c(153): 
error: identifier "M_PI" is undefined
t = tan (M_PI * sc_rand (state));
 ^

compilation aborted for 
/home/saspark2/build2//tmp/unpack/p4est-2.3.2/sc/src/sc_random.c (code 2)
make[1]: *** [src/libsc_la-sc_random.lo] Error 1
make[1]: *** Waiting for unfinished jobs
make: *** [all] Error 2
Error: Error in make sc

On Friday, March 4, 2022 at 2:20:50 PM UTC-7 Wolfgang Bangerth wrote:

>
> Stephanie,
>
> > They told me to reinstall using intel/2019.4 as it is more compatible 
> > with the setup they have. However in this second installation I'm having 
> > issues with what I think might be the intel compilers in installing 
> > p4est and subsequently deal.ii. I'm able to install all the other 
> > packages that I need.
>
> The issue you have here...
>
> > 
> /home/saspark2/build2//tmp/unpack/p4est-2.3.2/src/p8est_connectivity.c(930): 
>
> > error: expected an expression
> >   for (int i=0; i >^
>
> ...is that in traditional C, you cannot declare variables as part of a 
> 'for' loop like you can in C++. See also
>
>
> https://stackoverflow.com/questions/1287863/c-for-loop-int-initial-declaration
> You can do that since the 1999 C standard, which means that most 
> compilers now default to supporting this construct. Apparently the Intel 
> compiler is 23 years behind the times :-( Can you choose which version 
> of the Intel compiler you want to use? Maybe a newer version defaults to 
> C99.
>
> If you can't, can you try to do something like
> export CFLAGS="-std=c99"
> (or whatever flag the Intel compiler wants to select a specific language 
> standard) before you call the p4est configure script and before 
> compiling p4est?
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>

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[deal.II] University cluster installation issue: compilers

[Stephanie Sparks]

Hello,

I ran into an issue with my installation of deal.ii on my university 
cluster when attempting to run on multiple nodes using mpirun and the 
research computing team told me the issue was likely due to using 
openmpi/gcc.

They told me to reinstall using intel/2019.4 as it is more compatible with 
the setup they have. However in this second installation I'm having issues 
with what I think might be the intel compilers in installing p4est and 
subsequently deal.ii. I'm able to install all the other packages that I 
need.

I attached the configuration log in case that helps and copy the error 
output below.

Thanks,
Stephanie

/home/saspark2/build2//tmp/unpack/p4est-2.3.2/src/p8est_connectivity.c(930): 
error: expected an expression
  for (int i=0; ihttp://www.dealii.org/
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config.output
Description: Binary data

Re: [deal.II] Re: Cluster installation error with symengine library

[Stephanie Sparks]

Timo,

I did try to install from scratch and I'm getting the same error:

*Could not find the symengine library!*

*Please ensure that a suitable symengine library is installed on your 
computer.*

I turned off symengine in the candi.cfg file and deleted the installation 
library so I'm not sure what else to do. 

Thanks,
Stephanie
On Tuesday, February 15, 2022 at 1:42:34 PM UTC-7 Timo Heister wrote:

> Sure, the easiest is to start over and delete the whole installation 
> directory before you run Candi.
> You can try if it is enough to delete tmp/build/ but I am not sure.
>
> On Tue, Feb 15, 2022, 13:49 Stephanie Sparks  wrote:
>
>> Hi Timo,
>>
>> I did use candi to re-install without symengine and then when attempting 
>> to install deal.ii I got an error that symengine library could not be 
>> found. Is there a way to configure it such that symengine is not necessary 
>> for deal.ii?
>>
>> Thanks,
>> Stephanie
>>
>> On Tuesday, February 8, 2022 at 8:05:01 AM UTC-7 Timo Heister wrote:
>>
>>> Stephanie,
>>>
>>> I think you likely don't need some fine, am i right? Just comment out 
>>> the line for it in the candi.cfg and rerun the setup (you might need to 
>>> delete the tmp directory).
>>>
>>>
>>> On Tue, Feb 8, 2022, 10:01 Raghunandan Pratoori  
>>> wrote:
>>>
>>>> Hi Stephanie,
>>>>
>>>> I use a singularity container with deal.ii on my university cluster. I 
>>>> found it to be much simpler and working on any other cluster tried without 
>>>> any problems. I suggest you try that as it is a more reliable solution.
>>>> Also, if needed, I can give you access to the singularity container I 
>>>> built on Ubuntu 20.04 with deal.ii v9.3.0
>>>>
>>>> Best,
>>>> Raghunandan.
>>>>
>>>> On Tuesday, February 8, 2022 at 8:30:33 AM UTC-6 sasp...@asu.edu wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I am trying to install deal.ii on my university cluster and have been 
>>>>> successful up to this point; however, when I attempt to run examples I 
>>>>> get 
>>>>> the following error:
>>>>>
>>>>> ./step-1: error while loading shared libraries: libsymengine.so.0.7: 
>>>>> cannot open shared object file: No such file or directory
>>>>>
>>>>> I found an entry in the FAQ regarding similar problems with linking 
>>>>> PETSc and attempted to use that fix but I'm still running into the same 
>>>>> issue.
>>>>>
>>>>> Any help would be greatly appreciated.
>>>>>
>>>>> Thanks,
>>>>> Stephanie
>>>>>
>>>> -- 
>>>> The deal.II project is located at http://www.dealii.org/
>>>> For mailing list/forum options, see 
>>>> https://groups.google.com/d/forum/dealii?hl=en
>>>> --- 
>>>> You received this message because you are subscribed to the Google 
>>>> Groups "deal.II User Group" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send 
>>>> an email to dealii+un...@googlegroups.com.
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>>>> https://groups.google.com/d/msgid/dealii/61bc9eb6-a392-4b3a-836e-37764a389b0an%40googlegroups.com
>>>>  
>>>> <https://groups.google.com/d/msgid/dealii/61bc9eb6-a392-4b3a-836e-37764a389b0an%40googlegroups.com?utm_medium=email_source=footer>
>>>> .
>>>>
>>> -- 
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see 
>> https://groups.google.com/d/forum/dealii?hl=en
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> To view this discussion on the web visit 
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>>  
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>> .
>>
>

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Re: [deal.II] Re: Cluster installation error with symengine library

[Stephanie Sparks]

Hi Timo,

I did use candi to re-install without symengine and then when attempting to 
install deal.ii I got an error that symengine library could not be found. 
Is there a way to configure it such that symengine is not necessary for 
deal.ii?

Thanks,
Stephanie

On Tuesday, February 8, 2022 at 8:05:01 AM UTC-7 Timo Heister wrote:

> Stephanie,
>
> I think you likely don't need some fine, am i right? Just comment out the 
> line for it in the candi.cfg and rerun the setup (you might need to delete 
> the tmp directory).
>
>
> On Tue, Feb 8, 2022, 10:01 Raghunandan Pratoori  wrote:
>
>> Hi Stephanie,
>>
>> I use a singularity container with deal.ii on my university cluster. I 
>> found it to be much simpler and working on any other cluster tried without 
>> any problems. I suggest you try that as it is a more reliable solution.
>> Also, if needed, I can give you access to the singularity container I 
>> built on Ubuntu 20.04 with deal.ii v9.3.0
>>
>> Best,
>> Raghunandan.
>>
>> On Tuesday, February 8, 2022 at 8:30:33 AM UTC-6 sasp...@asu.edu wrote:
>>
>>> Hello,
>>>
>>> I am trying to install deal.ii on my university cluster and have been 
>>> successful up to this point; however, when I attempt to run examples I get 
>>> the following error:
>>>
>>> ./step-1: error while loading shared libraries: libsymengine.so.0.7: 
>>> cannot open shared object file: No such file or directory
>>>
>>> I found an entry in the FAQ regarding similar problems with linking 
>>> PETSc and attempted to use that fix but I'm still running into the same 
>>> issue.
>>>
>>> Any help would be greatly appreciated.
>>>
>>> Thanks,
>>> Stephanie
>>>
>> -- 
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see 
>> https://groups.google.com/d/forum/dealii?hl=en
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>>  
>> 
>> .
>>
>

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[deal.II] Cluster installation error with symengine library

[Stephanie Sparks]

Hello,

I am trying to install deal.ii on my university cluster and have been 
successful up to this point; however, when I attempt to run examples I get 
the following error:

./step-1: error while loading shared libraries: libsymengine.so.0.7: cannot 
open shared object file: No such file or directory

I found an entry in the FAQ regarding similar problems with linking PETSc 
and attempted to use that fix but I'm still running into the same issue.

Any help would be greatly appreciated.

Thanks,
Stephanie

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