Re: [Users] Error in thorn Vectors

[Hamilton, Maria]

?Ian,


Yes, all packages are installed. I am attaching the list of brewed packages.

However, when I test them, gcc and open-mpi are failing.


Here is the error:?


brew test gcc
Testing gcc
==> /usr/local/Cellar/gcc/7.2.0/bin/gcc-7 -o hello-c hello-c.c
==> /usr/local/Cellar/gcc/7.2.0/bin/g++-7 -o hello-cc hello-cc.cc
Last 15 lines from /Users/babiuc/Library/Logs/Homebrew/gcc/test.02.g++-7:
hello-cc.cc

In file included from 
/usr/local/Cellar/gcc/7.2.0/include/c++/7.2.0/ext/string_conversions.h:41:0,
 from 
/usr/local/Cellar/gcc/7.2.0/include/c++/7.2.0/bits/basic_string.h:6159,
 from /usr/local/Cellar/gcc/7.2.0/include/c++/7.2.0/string:52,
 from 
/usr/local/Cellar/gcc/7.2.0/include/c++/7.2.0/bits/locale_classes.h:40,
 from 
/usr/local/Cellar/gcc/7.2.0/include/c++/7.2.0/bits/ios_base.h:41,
 from /usr/local/Cellar/gcc/7.2.0/include/c++/7.2.0/ios:42,
 from /usr/local/Cellar/gcc/7.2.0/include/c++/7.2.0/ostream:38,
 from /usr/local/Cellar/gcc/7.2.0/include/c++/7.2.0/iostream:39,
 from hello-cc.cc:1:
/usr/local/Cellar/gcc/7.2.0/include/c++/7.2.0/cstdlib:75:15: fatal error: 
stdlib.h: No such file or directory
 #include_next 
   ^~
compilation terminated.
Error: gcc: failed

brew test open-mpi
Testing open-mpi
==> /usr/local/Cellar/open-mpi/3.0.0/bin/mpicc hello.c -o hello
==> ./hello
==> /usr/local/Cellar/open-mpi/3.0.0/bin/mpirun -np 4 ./hello
Last 15 lines from /Users/babiuc/Library/Logs/Homebrew/open-mpi/test.03.mpirun:
2017-11-14 11:04:49 -0500

/usr/local/Cellar/open-mpi/3.0.0/bin/mpirun
-np
4
./hello

--
There are not enough slots available in the system to satisfy the 4 slots
that were requested by the application:
  ./hello

Either request fewer slots for your application, or make more slots available
for use.
--
Error: open-mpi: failed
Failed executing: /usr/local/Cellar/open-mpi/3.0.0/bin/mpirun -np 4 ./hello


I am reinstalling them now, and test them again.

___
Dr. Maria C. Babiuc Hamilton
Department of Physics
Marshall University
S257 Science Building
Huntington, WV, 25755
Phone: (304)696-2754
https://works.bepress.com/maria_babiuc-hamilton/

From: Ian Hinder <ian.hin...@aei.mpg.de>
Sent: Tuesday, November 14, 2017 3:41 AM
To: Hamilton, Maria
Cc: Eloisa Bentivegna; Einstein Toolkit Users
Subject: Re: [Users] Error in thorn Vectors



On 14 Nov 2017, at 01:12, Hamilton, Maria 
<bab...@marshall.edu<mailto:bab...@marshall.edu>> wrote:

Hello,

Yes, previously I had the error in thorns Vectors, and I followed the 
suggestion to use the current stable version of Cactus.

I am not using simfactory, but this command:
make ET-config options=simfactory/mdb/optionlists/osx-homebrew.cfg 
THORNLIST=thornlists/einsteintoolkit.th<http://einsteintoolkit.th>

The error is:
checking for M_PI... no
configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to CPPFLAGS.

Here is what I tried to add to CPPFLAGS:
-D_USE_MATH_DEFINES
-D_XOPEN_SOURCE
-DM_PI = 3.14149265358979323847

I also tried to change c11 to c99 at CFLAGS and add
-stdlib=libc++ at LIBCXX.

None of those worked.

Please let me know what is to be done.

Hi Maria,

Have you installed all the homebrew packages listed at the top of 
osx-homebrew.cfg?

--
Ian Hinder
http://members.aei.mpg.de/ianhin



packages_installed
Description: packages_installed
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Re: [Users] Error in thorn Vectors

[Ian Hinder]

> On 14 Nov 2017, at 01:12, Hamilton, Maria  wrote:
> 
> Hello,
> 
> Yes, previously I had the error in thorns Vectors, and I followed the 
> suggestion to use the current stable version of Cactus.
> 
> I am not using simfactory, but this command:
> make ET-config options=simfactory/mdb/optionlists/osx-homebrew.cfg 
> THORNLIST=thornlists/einsteintoolkit.th
> 
> The error is: 
> checking for M_PI... no
> configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to CPPFLAGS.
> 
> Here is what I tried to add to CPPFLAGS:
> -D_USE_MATH_DEFINES
> -D_XOPEN_SOURCE
> -DM_PI = 3.14149265358979323847
> 
> I also tried to change c11 to c99 at CFLAGS and add 
> -stdlib=libc++ at LIBCXX.
> 
> None of those worked. 
> 
> Please let me know what is to be done.

Hi Maria,

Have you installed all the homebrew packages listed at the top of 
osx-homebrew.cfg?

-- 
Ian Hinder
http://members.aei.mpg.de/ianhin

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Re: [Users] Error in thorn Vectors

[Hamilton, Maria]

Hello,

Yes, previously I had the error in thorns Vectors, and I followed the 
suggestion to use the current stable version of Cactus.
 
I am not using simfactory, but this command:
make ET-config options=simfactory/mdb/optionlists/osx-homebrew.cfg 
THORNLIST=thornlists/einsteintoolkit.th

The error is: 
checking for M_PI... no
configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to CPPFLAGS.

Here is what I tried to add to CPPFLAGS:
 -D_USE_MATH_DEFINES
-D_XOPEN_SOURCE
-DM_PI = 3.14149265358979323847

I also tried to change c11 to c99 at CFLAGS and add 
-stdlib=libc++ at LIBCXX.

None of those worked. 

Please let me know what is to be done.

Thanks,
Maria

___
Dr. Maria C. Babiuc Hamilton
Department of Physics
Marshall University
S257 Science Building
Huntington, WV, 25755
Phone: (304)696-2754
https://works.bepress.com/maria_babiuc-hamilton/


From: users-boun...@einsteintoolkit.org <users-boun...@einsteintoolkit.org> on 
behalf of Eloisa Bentivegna <eloisa.bentive...@ct.infn.it>
Sent: Monday, November 13, 2017 1:51 PM
To: users@einsteintoolkit.org
Subject: Re: [Users] Error in thorn Vectors

On 13/11/17 16:02, Roland Haas wrote:
> Hello all,
>
> Maria has already created a ticket:
> https://trac.einsteintoolkit.org/ticket/2084

True, but this is a separate issue (not with Vectors but with the
configuration stage on a clean checkout, it seems).

My suspicion is that the homebrew instructions in the tutorial may have
become outdated, and that we need to add some options to make sure the
math libs are installed, and found at configure time.

Unfortunately I use neither High Sierra nor Homebrew, so I have no way
to check myself.

Eloisa
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Re: [Users] Error in thorn Vectors

[Roland Haas]

Hello all,

Maria has already created a ticket:
https://trac.einsteintoolkit.org/ticket/2084

Yours,
Roland

> On 10/11/17 22:34, Hamilton, Maria wrote:
> > Hello Eloisa,
> > 
> > This is strange. I did do a fresh checkout and tried to compile it with the 
> > osx-homebrew.cfg but I am getting this error:
> > 
> > checking for M_PI... no
> > configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to CPPFLAGS.
> > 
> > I added the flag to CPPFLAGS, I even added a new flag 
> > FDBITSFLAGS="-D_XOPEN_SOURCE=500 which I found on the internet, but the 
> > same error persisted. 
> > 
> > I am running Cactus on a Mac Laptop, OSX High Sierra and recommended brewed 
> > packages including gcc 7.2.0
> > 
> > Please let me know how to fix it.  
> 
> Dear Maria,
> 
> if you're following a tutorial (say, the one at
> https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users),
> please open a ticket to report which set of instructions do not work on
> your system.
> 
> For instance, are you using Simfactory? Where exactly did you modify
> CPPFLAGS?
> 
> Best,
> Eloisa
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-- 
My email is as private as my paper mail. I therefore support encrypting
and signing email messages. Get my PGP key from http://keys.gnupg.net.


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Re: [Users] Error in thorn Vectors

[Eloisa Bentivegna]

On 10/11/17 22:34, Hamilton, Maria wrote:
> Hello Eloisa,
> 
> This is strange. I did do a fresh checkout and tried to compile it with the 
> osx-homebrew.cfg but I am getting this error:
> 
> checking for M_PI... no
> configure: error: M_PI not defined. Try adding -D_XOPEN_SOURCE to CPPFLAGS.
> 
> I added the flag to CPPFLAGS, I even added a new flag 
> FDBITSFLAGS="-D_XOPEN_SOURCE=500 which I found on the internet, but the same 
> error persisted. 
> 
> I am running Cactus on a Mac Laptop, OSX High Sierra and recommended brewed 
> packages including gcc 7.2.0
> 
> Please let me know how to fix it.

Dear Maria,

if you're following a tutorial (say, the one at
https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users),
please open a ticket to report which set of instructions do not work on
your system.

For instance, are you using Simfactory? Where exactly did you modify
CPPFLAGS?

Best,
Eloisa
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Re: [Users] Error in thorn Vectors

[Eloisa Bentivegna]

On 06/11/17 20:09, Hamilton, Maria wrote:
> Hello Eloisa,
> 
> From my memory I'd say I am using the development version. 
> Is there a way to check this out?

Hi!

Since the ET is hosted in a collection of repositories, the direct way
would be to check which branch of each you're on. Alternatively, you can
simply start with a fresh checkout (of, say, the last release) and see
if you encounter the same problem.

I am posting this to the list in case someone else has a better
solution. In any case, please include this information when you open the
ticket.

> I tried to open ticket at: https://trac.einsteintoolkit.org, but I got this 
> message:
> Submission rejected as potential spam

I am not sure why this happens. Did you post as anonymous, or included
your (institutional) address email in the Reporter field?

Eloisa
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Re: [Users] Error in thorn Vectors

[Erik Schnetter]

These intrinsics are not available in the SSE2 extensions, and a respective
#ifdef is missing. I believe this has been corrected on a branch, but
apparently not yet in the main version of this thorn. Please open a ticket
for this.

-erik

On Mon, Nov 6, 2017 at 10:04 AM, Hamilton, Maria 
wrote:

> After the last Cactus update, I got this error:
>
>
>
> Checking status of thorn Vectors
> COMPILING arrangements/CactusUtils/Vectors/src/vectors.cc
> In file included from /Users/babiuc/Cactus/arrangements/CactusUtils/
> Vectors/src/vectors.h:18:0,
>  from /Users/babiuc/Cactus/arrangements/CactusUtils/
> Vectors/src/vectors.cc:1:
> /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors-4-SSE.h:
> In function 'CCTK_REAL4 k4sum(CCTK_REAL4_VEC)':
> /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors-4-SSE.h:709:29:
> error: '_mm_hadd_ps' was not declared in this scope
>CCTK_REAL4_VEC const x2 = _mm_hadd_ps(x1, x1);
>  ^~~
> /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors-4-SSE.h:709:29:
> note: suggested alternative: '_mm_add_ps'
>CCTK_REAL4_VEC const x2 = _mm_hadd_ps(x1, x1);
>  ^~~
>  _mm_add_ps
> In file included from /Users/babiuc/Cactus/arrangements/CactusUtils/
> Vectors/src/vectors.h:30:0,
>  from /Users/babiuc/Cactus/arrangements/CactusUtils/
> Vectors/src/vectors.cc:1:
> /Users/babiuc/Cactus/arrangements/CactusUtils/Vectors/src/vectors-8-SSE2.h:
> In function 'CCTK_REAL8 k8sum(CCTK_REAL8_VEC)':
> /Users/babiuc/Cactus/arrangements/CactusUtils/
> Vectors/src/vectors-8-SSE2.h:753:29: error: '_mm_hadd_pd' was not
> declared in this scope
>CCTK_REAL8_VEC const x2 = _mm_hadd_pd(x1, x1);
>  ^~~
> /Users/babiuc/Cactus/arrangements/CactusUtils/
> Vectors/src/vectors-8-SSE2.h:753:29: note: suggested alternative:
> '_mm_add_pd'
>CCTK_REAL8_VEC const x2 = _mm_hadd_pd(x1, x1);
>  ^~~
>  _mm_add_pd
> make[4]: *** [vectors.cc.o] Error 1
> make[3]: *** [make.checked] Error 2
> make[2]: *** [/Users/babiuc/Cactus/configs/ET/lib/libthorn_Vectors.a]
> Error 2
> make[1]: *** [ET] Error 2
> make: *** [ET-rebuild] Error 2​
>
>
> Please advise.
>
>
> thank you,
>
> Maria
> ​
>
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>


-- 
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Re: [Users] Error in thorn Vectors

[Eloisa Bentivegna]

On 06/11/17 16:04, Hamilton, Maria wrote:
> After the last Cactus update, I got this error:

Hi Maria,

could you clarify what version of the code you're using? Are you on a
specific release?

Eloisa
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