[Users] Compilation Error in cluster ParamGanga
Shamim Haque 1910511
shamims at iiserb.ac.in
Wed May 31 16:26:38 CDT 2023
Hello All,
I have made little progress on compiling ETK on this cluster, as the admins
allowed me to compile ETK on the login node. I am finding new errors and am
unable to debug the issue. I am trying to configure ETK using Intel19, and
the error says the following:
*/home/shamims.iiserb/ET_debug/Cactus/arrangements/Carpet/CarpetMask/src/mask_surface.cc(160):
error: more than one instance of overloaded function "CarpetMask::isnan"
matches the argument list: function "isnan(double)"
function "std::isnan(double)" argument types are: (CCTK_REAL8)
assert(not isnan(phi)); ^compilation aborted for
/home/shamims.iiserb/ET_debug/Cactus/configs/sim/build/CarpetMask/mask_surface.cc
(code 2)make[3]: *** [mask_surface.cc.o] Error 2make[2]: *** [make.checked]
Error 2make[1]: ***
[/home/shamims.iiserb/ET_debug/Cactus/configs/sim/lib/libthorn_CarpetMask.a]
Error 2make: *** [sim] Error 2*
I have attached the machinefile, optionlist, config log and full output
file for reference. I configured the scripts using the available example
optionlist and machinefile for supermuc_ng and stampede2. Please let me
know if more info is required, and thanks in advance for your help.
Regards
Shamim Haque
Senior Research Fellow (SRF)
Department of Physics
IISER Bhopal
ᐧ
On Fri, May 19, 2023 at 2:32 PM Shamim Haque 1910511 <shamims at iiserb.ac.in>
wrote:
> Hello Roland,
>
> Thank you for the reply. Yes, I am trying to compile ETK in the computing
> node via sbatch queue. I am in touch with the system admin to resolve
> the issue with the compilers.
>
> Regards
> Shamim Haque
> Senior Research Fellow (SRF)
> Department of Physics
> IISER Bhopal
>
> ᐧ
>
> On Thu, May 18, 2023 at 7:32 PM Roland Haas <rhaas at illinois.edu> wrote:
>
>> Hello Shamin,
>>
>> A missing math.h would point to a faulty compiler installation. Since
>> you are trying to compile (are you?) ona compute node in a running job,
>> my guess would be that the cluster admins are not providing compilers
>> on the compute nodes but only on the login nodes.
>>
>> This would be something to contact your cluster's help desk about.
>>
>> Yours,
>> Roland
>>
>> > Hello Roland,
>> >
>> > I did try that fix; the error remains the same. Actually, we landed on
>> an
>> > even more primitive problem, where Steve suggested a basic test, that
>> is to
>> > compile the following code:
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > *#include <math.h>#include <stdio.h>int main() { printf("%f\n",
>> > M_PI); return 0;}*
>> >
>> > This program compiles just fine in the login node but gives out the
>> > following error while compiling it via jobscript submission in the
>> sbatch
>> > queue:
>> >
>> > prog.cpp:1:18: fatal error: math.h: No such file or directory
>> > #include <math.h>
>> > ^
>> > compilation terminated.
>> >
>> > ----OR-----
>> >
>> >
>> /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10:
>> > fatal error: features.h: No such file or directory
>> > 39 | #include <features.h>
>> > | ^~~~~~~~~~~~
>> > compilation terminated.
>> >
>> > I have reported this problem to the HPC admin and await their response.
>> >
>> > Regards
>> > Shamim Haque
>> > Senior Research Fellow (SRF)
>> > Department of Physics
>> > IISER Bhopal
>> >
>> > ᐧ
>> >
>> > On Fri, May 12, 2023 at 12:20 AM Roland Haas <rhaas at illinois.edu>
>> wrote:
>> >
>> > > Hello all,
>> > >
>> > > Since the error is a missing M_PI and the configure script already
>> > > gives a suggested fix:
>> > >
>> > > Try adding -D_XOPEN_SOURCE to CPPFLAGS.
>> > >
>> > > have you tried adding:
>> > >
>> > > CPPFLAGS=-D_XOPEN_SOURCE
>> > >
>> > > to your option list file before compiling?
>> > >
>> > > Yours,
>> > > Roland
>> > >
>> > > > Thanks Steve. I have raised complaint to the admin about this issue.
>> > > >
>> > > > On Thu, May 11, 2023, 11:18 PM Steven R. Brandt <
>> sbrandt at cct.lsu.edu>
>> > > wrote:
>> > > >
>> > > > > I would talk to the system administrators about that. There is
>> > > definitely
>> > > > > something wrong with your compiler install if you can't find
>> math.h.
>> > > > >
>> > > > > --Steve
>> > > > > On 5/11/2023 2:02 AM, Shamim Haque 1910511 wrote:
>> > > > >
>> > > > > Dear Steve,
>> > > > >
>> > > > > I just rechecked the cpp program to output M_PI in the computing
>> nodes,
>> > > > > and that is not working right now, which was somehow working fine
>> a few
>> > > > > days ago. I also tried different gcc versions (4.8, 10.2, 11.1,
>> > > gnu8/8.3)
>> > > > > available in the cluster. All report similar issue:
>> > > > >
>> > > > > prog.cpp:1:18: fatal error: math.h: No such file or directory
>> > > > > #include <math.h>
>> > > > > ^
>> > > > > compilation terminated.
>> > > > >
>> > > > > ----OR-----
>> > > > >
>> > > > >
>> > >
>> /home/apps/gcc-10.2.0/include/c++/10.2.0/x86_64-pc-linux-gnu/bits/os_defines.h:39:10:
>>
>> > > > > fatal error: features.h: No such file or directory
>> > > > > 39 | #include <features.h>
>> > > > > | ^~~~~~~~~~~~
>> > > > > compilation terminated.
>> > > > >
>> > > > > The cpp code seems to work fine in login node, as it gives out
>> the
>> > > value
>> > > > > of pi upon execution. I am contacting the hpc admin to resolve
>> this
>> > > issue.
>> > > > >
>> > > > > I am attaching the test code (prog.cpp), the sbatch jobscript
>> (prog.sh)
>> > > > > and the output file (slurn-117473.out), if you would like to have
>> a
>> > > look at
>> > > > > it.
>> > > > >
>> > > > > Please let me know if I should try something different to get
>> this
>> > > working.
>> > > > >
>> > > > > Regards
>> > > > > Shamim Haque
>> > > > > Senior Research Fellow (SRF)
>> > > > > Department of Physics
>> > > > > IISER Bhopal
>> > > > >
>> > > > > ᐧ
>> > > > >
>> > > > > On Mon, May 8, 2023 at 7:25 PM Shamim Haque 1910511 <
>> > > shamims at iiserb.ac.in>
>> > > > > wrote:
>> > > > >
>> > > > >> Thanks Steve. I'll make the changes and try again. I'll let you
>> know
>> > > the
>> > > > >> outcome.
>> > > > >>
>> > > > >> Regards
>> > > > >> Shamim Haque
>> > > > >> Senior Research Fellow (SRF)
>> > > > >> Department of Physics
>> > > > >> IISER Bhopal
>> > > > >>
>> > > > >> ᐧ
>> > > > >>
>> > > > >> On Mon, May 8, 2023 at 7:21 PM Steven R. Brandt <
>> sbrandt at cct.lsu.edu>
>> > > > >> wrote:
>> > > > >>
>> > > > >>> That tends to make me think you aren't using the compiler you
>> think
>> > > > >>> you're using. You could put full paths in the .cfg files and
>> > > recompile from
>> > > > >>> scratch.
>> > > > >>>
>> > > > >>> i.e.
>> > > > >>>
>> > > > >>> CXX = /full/path/to/icc
>> > > > >>>
>> > > > >>> --Steve
>> > > > >>> On 5/3/2023 3:26 PM, Shamim Haque 1910511 wrote:
>> > > > >>>
>> > > > >>> Yes, this gives the value of Pi successfully, before starting
>> the
>> > > > >>> compilation:
>> > > > >>>
>> > > > >>>
>> > > > >>>
>> > > > >>>
>> > > > >>>
>> > > > >>>
>> > > > >>>
>> > > > >>>
>> > > > >>>
>> > > > >>> */home/vkerni.iitr/sam/trial 3.141593 Current machine:
>> paramganga3
>> > > Using
>> > > > >>> configuration: sim Reconfiguring sim Writing configuration to:
>> > > > >>> /home/vkerni.iitr/sam/ET_debug/Cactus/configs/sim/OptionList
>> Cactus -
>> > > > >>> version: 4.12.0 Reconfiguring sim. *
>> > > > >>> *.*
>> > > > >>> *.*
>> > > > >>> *.*
>> > > > >>>
>> > > > >>>
>> > > > >>>
>> > > > >>>
>> > > > >>>
>> > > > >>> *checking for M_PI... no configure: error: M_PI not defined.
>> Try
>> > > adding
>> > > > >>> -D_XOPEN_SOURCE to CPPFLAGS. Error reconfiguring sim-config
>> make: ***
>> > > > >>> [sim-config] Error 2 *
>> > > > >>>
>> > > > >>>
>> > > > >>> Shamim Haque
>> > > > >>> Senior Research Fellow (SRF)
>> > > > >>> Department of Physics
>> > > > >>> IISER Bhopal
>> > > > >>>
>> > > > >>> ᐧ
>> > > > >>>
>> > > > >>> On Thu, May 4, 2023 at 12:29 AM Steven Brandt <
>> sbrandt at cct.lsu.edu>
>> > > > >>> wrote:
>> > > > >>>
>> > > > >>>> So, sanity check, can you compile the following program
>> outside of
>> > > > >>>> Cactus?
>> > > > >>>>
>> > > > >>>> #include <math.h>
>> > > > >>>> #include <stdio.h>
>> > > > >>>>
>> > > > >>>> int main() {
>> > > > >>>> printf("%f\n", M_PI);
>> > > > >>>> return 0;
>> > > > >>>> }
>> > > > >>>> On 5/3/2023 1:50 PM, Shamim Haque 1910511 wrote:
>> > > > >>>>
>> > > > >>>> Dear Steve,
>> > > > >>>>
>> > > > >>>> I tried gcc (10 and 11) as well and I am stuck with the
>> following
>> > > error:
>> > > > >>>> *configure: error: M_PI not defined. Try adding
>> -D_XOPEN_SOURCE to
>> > > > >>>> CPPFLAGS.*
>> > > > >>>>
>> > > > >>>> This also happened for Intel (2020 and 2019). I have attached
>> both
>> > > the
>> > > > >>>> output files here.
>> > > > >>>>
>> > > > >>>> Please ignore the out file in the first email, I have
>> uploaded
>> > > another
>> > > > >>>> out file by mistake. The rest of the files are correct in the
>> first
>> > > mail.
>> > > > >>>>
>> > > > >>>> Regards
>> > > > >>>> Shamim Haque
>> > > > >>>> Senior Research Fellow (SRF)
>> > > > >>>> Department of Physics
>> > > > >>>> IISER Bhopal
>> > > > >>>>
>> > > > >>>> ᐧ
>> > > > >>>>
>> > > > >>>> On Wed, May 3, 2023 at 8:04 PM Steven Brandt <
>> sbrandt at cct.lsu.edu>
>> > > > >>>> wrote:
>> > > > >>>>
>> > > > >>>>> I notice from the output that your compiler claims "limits.h"
>> is
>> > > > >>>>> missing. Possibly there's something wrong with your icc
>> setup?
>> > > Maybe you
>> > > > >>>>> should try using gcc / gfortran instead.
>> > > > >>>>>
>> > > > >>>>> --Steve
>> > > > >>>>> On 5/3/2023 8:20 AM, Shamim Haque 1910511 wrote:
>> > > > >>>>>
>> > > > >>>>> Dear Frank,
>> > > > >>>>>
>> > > > >>>>> I added the alias pattern for the computing nodes and now ETK
>> can
>> > > > >>>>> detect the cluster (checked by asking "whoami") during the
>> batch
>> > > queuing.
>> > > > >>>>> I'll get in touch with the admins to include 'patch'.
>> > > > >>>>>
>> > > > >>>>> However, the problem still persists, having assured that the
>> > > correct
>> > > > >>>>> machine file and option list are being used during the
>> compilation.
>> > > > >>>>>
>> > > > >>>>> Regards
>> > > > >>>>> Shamim Haque
>> > > > >>>>> Senior Research Fellow (SRF)
>> > > > >>>>> Department of Physics
>> > > > >>>>> IISER Bhopal
>> > > > >>>>>
>> > > > >>>>> ᐧ
>> > > > >>>>>
>> > > > >>>>> On Wed, May 3, 2023 at 3:49 PM Frank Loeffler <
>> > > > >>>>> frank.loeffler at uni-jena.de> wrote:
>> > > > >>>>>
>> > > > >>>>>> Hi Shamim
>> > > > >>>>>>
>> > > > >>>>>> On Wed, May 03, 2023 at 03:11:49PM +0530, Shamim Haque
>> 1910511
>> > > wrote:
>> > > > >>>>>> >We are trying to compile ETK on ParamGanga at IIT Roorkee.
>> The
>> > > > >>>>>> >compilation
>> > > > >>>>>> >stops at a very initial step and gives out the error:
>> > > > >>>>>> >
>> > > > >>>>>> >*checking whether the Fortran compiler (gfortran )
>> works...
>> > > > >>>>>> yeschecking
>> > > > >>>>>> >whether the Fortran compiler (gfortran ) is a
>> > > cross-compiler...
>> > > > >>>>>> nochecking
>> > > > >>>>>> >whether the Fortran compiler (gfortran ) supports TYPE(*)
>> for
>> > > > >>>>>> >CCTK_PointerTo... yeschecking how to run the C
>> preprocessor...
>> > > > >>>>>> cppchecking
>> > > > >>>>>> >for ANSI C header files... nochecking for C99 features...
>> > > > >>>>>> yeschecking for
>> > > > >>>>>> >M_PI... noconfigure: error: M_PI not defined. Try adding
>> > > > >>>>>> -D_XOPEN_SOURCE to
>> > > > >>>>>> >CPPFLAGS.*
>> > > > >>>>>> >
>> > > > >>>>>> >We tried adding -D_XOPEN_SOURCE to CPPFLAGS, but it does
>> not
>> > > help.
>> > > > >>>>>> This
>> > > > >>>>>> >error is consistent if we set up using Intel Compiler (2020
>> or
>> > > > >>>>>> 2019), or
>> > > > >>>>>> >gcc (11 or 10). I have attached the outfile, error file,
>> > > machine
>> > > > >>>>>> script,
>> > > > >>>>>> >and option lists for both cases (Intel and gcc) for any
>> > > reference.
>> > > > >>>>>> >
>> > > > >>>>>> >Secondly, we are not allowed to compile ETK on login nodes.
>> So
>> > > we are
>> > > > >>>>>> >queuing a job script, which upon execution, enters the
>> Cactus
>> > > > >>>>>> directory,
>> > > > >>>>>> >does "setup-silent", and then executes the build command.
>> Is
>> > > this
>> > > > >>>>>> the right
>> > > > >>>>>> >way to compile ETK using the batch script? Or should we do
>> > > something
>> > > > >>>>>> >different? I have attached the shell script (compile.sh)
>> used
>> > > for
>> > > > >>>>>> sbatch
>> > > > >>>>>> >queue for reference.
>> > > > >>>>>>
>> > > > >>>>>> I might be wrong, but setup-silent will not use your machine
>> file
>> > > > >>>>>> which
>> > > > >>>>>> contains all the compiler flags, but will setup something
>> "from
>> > > > >>>>>> scratch"
>> > > > >>>>>> instead. According to the logs, this will be, e.g., in
>> > > > >>>>>>
>> > > > >>>>>>
>> > > > >>>>>>
>> > >
>> /home/shamims.iiserb/ET_debug/Cactus/repos/simfactory2/mdb/machines/cn139.iitr.ac.in.ini
>>
>> > > > >>>>>>
>> > > > >>>>>> My guess would be that this misses the compiler flags
>> necessary to
>> > > > >>>>>> have
>> > > > >>>>>> M_PI defined. The best way to get this working might be to
>> let
>> > > > >>>>>> simfactory also detect the cluster configuration on the
>> compute
>> > > nodes
>> > > > >>>>>> (where you compile), such that setup-silent is not needed,
>> but
>> > > > >>>>>> instead
>> > > > >>>>>> the correct cluster configuration is found and used
>> > > automatically. In
>> > > > >>>>>> order to do that, look at examples of 'aliaspattern' in the
>> > > > >>>>>> mdb/machines
>> > > > >>>>>> directory. An alternative would be to tell simfactory
>> specifically
>> > > > >>>>>> that
>> > > > >>>>>> you want to use your machine configuration file.
>> > > > >>>>>>
>> > > > >>>>>> As a side-note: I noticed the command 'patch' is missing
>> too.
>> > > This is
>> > > > >>>>>> a
>> > > > >>>>>> tool so common that it should be installed everywhere. Your
>> admin
>> > > is
>> > > > >>>>>> probably the best person to ask for advise here. It should
>> not be
>> > > too
>> > > > >>>>>> hard to install yourself, but that should not be necessary
>> either,
>> > > > >>>>>> especially when you are told to compile on compute nodes.
>> > > > >>>>>>
>> > > > >>>>>> Frank
>> > > > >>>>>>
>> > > > >>>>>>
>> > > > >>>>> _______________________________________________
>> > > > >>>>> Users mailing listUsers at einsteintoolkit.orghttp://
>> > > lists.einsteintoolkit.org/mailman/listinfo/users
>> > > > >>>>>
>> > > > >>>>> _______________________________________________
>> > > > >>>>> Users mailing list
>> > > > >>>>> Users at einsteintoolkit.org
>> > > > >>>>>
>> > >
>> https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinfo/users__;!!DZ3fjg!4xAKSrBYUo_v8jHEbenNg6aQ99Oq9QyeXsjq766lVDVwHAhFJODYjSU6XryKp264bQqDmBcTIA4Srkc4wOCn$
>>
>> > > > >>>>>
>> > > > >>>>
>> > >
>> > >
>> > > Yours,
>> > > Roland
>> > >
>> > > --
>> > > My email is as private as my paper mail. I therefore support
>> encrypting
>> > > and signing email messages. Get my PGP key from
>> https://urldefense.com/v3/__http://pgp.mit.edu__;!!DZ3fjg!5ZGhPGL_16Uj1eN8xbeLFN1po4t2MOETlRoEnO3fr4pBXNdsn_VXBbuywp1tgk0zKYy_oBKphC1Ny-KY0Vh9$
>> .
>> > >
>>
>> --
>> My email is as private as my paper mail. I therefore support encrypting
>> and signing email messages. Get my PGP key from http://pgp.mit.edu .
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>
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