[Users] Compilation Error in cluster ParamGanga
Shamim Haque 1910511
shamims at iiserb.ac.in
Mon Jun 19 09:21:41 CDT 2023
Dear Roland, Steve and Frank,
I am able to compile ETK properly with GNU compiler 8.3.0. The simulations
are also running successfully.
For Intel, the licence issue was cleared after using -j1, but there are a
few issues with other libraries, so I have stopped exploring this
route right now, maybe I'll try it later.
Thank you for all the help.
Regards
Shamim Haque
Senior Research Fellow (SRF)
Department of Physics
IISER Bhopal
ᐧ
On Tue, Jun 6, 2023 at 6:56 PM Roland Haas <rhaas at illinois.edu> wrote:
> Hello Shamim Haque,
>
> "icpc unable to checkout FLEXlm license" is caused by the compiler
> being unable to contact the license server. This is unrelated to the
> C++ compilation issue really.
>
> To be sure:
>
> * the only thing you did was add
> "-gxx-name=/opt/ohpc/pub/compiler/gcc/8.3.0/bin/g++" was it? In
> particular you did not add / remove any "module load" commands (e.g.,
> added a module load gcc after an existing module load intel)? I am
> asking b/c module load gcc may unload the intel compiler module and
> unset the environment variable that the Intel compiler uses to
> determine how to contact the license server.
>
> * you may also try to compile with just "make -j1" or
> "simfactory/bin/sim build -j1" to use only a single compiler instance
> in case the number of compiler licenses available is limited or the
> license server overwhelmed by too many concurrent compilations (by
> you or other users of the cluster)
>
> The issue with fftw3 and using gcc is that fftw3 (you are using a
> system provided fftw3? Either from a module or otherwise provided by
> the admin) has been compiled with the Intel compiler and thus cannot be
> used with the GNU compiler. You an set "FFTW_DIR = BUILD" to make the
> Einstein Toolkit build a copy from scratch using an included tar file.
> Not that this may be the case for other libraries as well. In
> particular you usually need to ensure that the MPI library used was
> compiled with the same compiler you use to compile the simulation code.
>
> Yours,
> Roland
>
> > Hello Roland,
> >
> > Thank you for the reply.
> >
> > I pointed -gxx-name to gcc/8.3.0, which resulted in an error related to
> the
> > "icpc unable to checkout FLEXlm license". I also tried to use a
> > different intel compiler (and point -gxx-name to gcc/11.1.0) to check if
> > the error can go away, but it remains the same. I communicated this to
> the
> > HPC admin and awaiting their response; please let me know if I should fix
> > something in my configuration. I have attached the out file
> > (intel_compile.out), config log (intel_config.log),
> > and optionlist (intel.cfg) for reference.
> >
> > Meanwhile, I also attempted to configure ET with gcc/11.1.0, which
> resulted
> > in some issues regarding the FFTW3. I have contacted the admins regarding
> > this, but please let me know if it is something to be fixed within the
> > optionlist. I have attached the out file (gcc_compile.out), config log
> > (gcc_config.log), and optionlist (gcc.cfg) for reference.
> >
> > The error in the output file says the following:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *Formaline: is still running, e.g. the final link stage.)/usr/bin/ld:
> > warning: libimf.so, needed by /home/apps/fftw3/fftw3.3.8/lib/libfftw3.so,
> > not found (try using -rpath or -rpath-link)/usr/bin/ld: warning:
> > libsvml.so, needed by /home/apps/fftw3/fftw3.3.8/lib/libfftw3.so, not
> found
> > (try using -rpath or -rpath-link)/usr/bin/ld: warning: libirng.so, needed
> > by /home/apps/fftw3/fftw3.3.8/lib/libfftw3.so, not found (try using
> -rpath
> > or -rpath-link)/usr/bin/ld: warning: libintlc.so.5, needed by
> > /home/apps/fftw3/fftw3.3.8/lib/libfftw3.so, not found (try using -rpath
> or
> > -rpath-link)/usr/bin/ld: warning: libgfortran.so.3, needed by
> > /lib/../lib64/liblapack.so, may conflict with
> > libgfortran.so.5/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so: undefined
> > reference to
> > `__intel_cpu_features_init_x'/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so:
> > undefined reference to
> > `__svml_sincos2'/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so: undefined
> > reference to
> > `_intel_fast_memset'/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so: undefined
> > reference to
> >
> `__intel_cpu_feature_indicator_x'/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so:
> > undefined reference to
> > `_intel_fast_memmove'/home/apps/fftw3/fftw3.3.8/lib/libfftw3.so:
> undefined
> > reference to `_intel_fast_memcpy'*
> >
> > Thanks in advance for all the help.
> >
> > Regards
> > Shamim
> >
> > ᐧ
> >
> > On Fri, Jun 2, 2023 at 1:31 AM Roland Haas <rhaas at illinois.edu> wrote:
> >
> > > Hello Shamim Haque,
> > >
> > > This most likely is caused by not having a full C++11 software stack
> > > enabled.
> > >
> > > The Intel compiler always uses the C++ STL library of the GNU g++
> > > compiler and must be matched up with a compatible g++ compiler's STL
> > > to correctly support C++11.
> > >
> > > This ticket (the last of many, hopefully) contains details:
> > >
> > >
> > >
> https://urldefense.com/v3/__https://bitbucket.org/einsteintoolkit/tickets/issues/2663/add-an-notice-about-minimum-intel-gcc__;!!DZ3fjg!4Z697XBz_Q8JIQSrOykhIqb_thU0tH0XLyTUT1zDMwhZlk1earaaKDJXweGCrJ3LGb2HvWAHbeRBlRGRwlyl$
> > >
> > > Basically, the fix is to find a gcc compiler at least version 6 on your
> > > cluster, then pass the option
> > >
> > > -gxx-name PATH-TO-GXX
> > >
> > > to icpc in the CXXFLAGS option list variable (see eg
> > >
> > >
> https://urldefense.com/v3/__https://bitbucket.org/simfactory/simfactory2/src/7e2592d264b1afe9ca2cb54bcab8dd9e4165cf98/mdb/optionlists/smic-openmpi.cfg?at=master*smic-openmpi.cfg-15:16__;Iw!!DZ3fjg!4Z697XBz_Q8JIQSrOykhIqb_thU0tH0XLyTUT1zDMwhZlk1earaaKDJXweGCrJ3LGb2HvWAHbeRBlSBbGTFf$
> > > ).
> > >
> > > If there is no gcc compiler version 6 or newer installed in the system,
> > > you will have to contact the administrators and ask them about it.
> > >
> > > The demo code in the description of
> > >
> https://urldefense.com/v3/__https://bitbucket.org/cactuscode/cactus/pull-requests/152__;!!DZ3fjg!4Z697XBz_Q8JIQSrOykhIqb_thU0tH0XLyTUT1zDMwhZlk1earaaKDJXweGCrJ3LGb2HvWAHbeRBlUmecdAQ$
> may help
> > > demonstrate to the admins what the issue is.
> > >
> > > Yours,
> > > Roland
> > >
> > > > 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
> > >
> https://urldefense.com/v3/__http://pgp.mit.edu__;!!DZ3fjg!9Rc70AgC5_rUJApjF6bdaoR4iJf6WXHxF1UsHWThqJwM8QxTwHKDWcVgn0kphw4Lmahcfk5a8gMIPSpV8TMD$
> > > .
> > > > >>
> > > > >
> > >
> > >
> > > --
> > > 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!4Z697XBz_Q8JIQSrOykhIqb_thU0tH0XLyTUT1zDMwhZlk1earaaKDJXweGCrJ3LGb2HvWAHbeRBlS57nxFF$
> .
> > >
>
>
> Yours,
> Roland
>
> --
> 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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