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@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://bitbucket.org/einsteintoolkit/tickets/issues/2663/add-an-notice-abou...
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://bitbucket.org/simfactory/simfactory2/src/7e2592d264b1afe9ca2cb54bcab... ).
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://bitbucket.org/cactuscode/cactus/pull-requests/152 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@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@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@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@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@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@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@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@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@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@einsteintoolkit.orghttp:// lists.einsteintoolkit.org/mailman/listinfo/users > >>>>> > >>>>> _______________________________________________ > >>>>> Users mailing list > >>>>> Users@einsteintoolkit.org > >>>>>
https://urldefense.com/v3/__http://lists.einsteintoolkit.org/mailman/listinf...
> >>>>> > >>>>
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_16Uj1eN8xb...
.
-- 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_rUJApjF6... .
-- 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 .