Maketools Error

Robert Steele II

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Jun 20, 2019, 6:21:55 PM6/20/19

to Nek5000

Hello Everyone,

I am new to using Nek5000 and I'm trying to mount the program onto an Apple I received. I get many errors and warnings when I try to compile genmap (per the Quickstart instructions), and also get an error which may or may not be related when I attempt to ./maketools all in the /tools folder. My error messages are listed below. Any help would be appreciated. Thanks!

Rob

[robertwatkinssteeleii][~/Nek5000/tools]> ./maketools genmap

----------------------

Make genmap...

----------------------

/opt/moose/mpich-3.3/clang-8.0.0/bin/mpif90 -c -DMAXNEL=150000 -cpp -fdefault-real-8 genmap.f

genmap.f:886:18:

len = indx1(prompt,'$',1) - 1

1

Warning: Rank mismatch in argument 's1' at (1) (scalar and rank-1) [-Wargument-mismatch]

genmap.f:220:24:

call linearmsh(cell,nelv,nelt,ndim)

1

Error: Actual argument contains too few elements for dummy argument 'cell' (1/2) at (1)

genmap.f:375:27:

call cscan(string,'MESH DATA',9)

1

Warning: Character length of actual argument shorter than of dummy argument 'ke' (9/80) at (1) [-Wargument-mismatch]

genmap.f:3292:9:

$ ('Error opening file in open_bin_file ',ierr)

1

Warning: Character length of actual argument shorter than of dummy argument 'name' (36/40) at (1) [-Wargument-mismatch]

genmap.f:3295:9:

$ ('Error reading header in open_bin_file ',ierr)

1

Warning: Character length of actual argument shorter than of dummy argument 'name' (38/40) at (1) [-Wargument-mismatch]

genmap.f:3211:10:

$ ('Error byte_reverse in buf_to_xy ',ierr)

1

Warning: Character length of actual argument shorter than of dummy argument 'name' (32/40) at (1) [-Wargument-mismatch]

genmap.f:3214:21:

call copyi4(igroup,buf(0),1) !0-1

1

Warning: Rank mismatch in argument 'a' at (1) (rank-1 and scalar) [-Wargument-mismatch]

genmap.f:3216:72:

call copy (xc,buf( 2),8) !2 --17

1

Warning: Type mismatch in argument 'y' at (1); passed INTEGER(4) to REAL(8) [-Wargument-mismatch]

genmap.f:3217:72:

call copy (yc,buf(18),8) !18--33

1

Warning: Type mismatch in argument 'y' at (1); passed INTEGER(4) to REAL(8) [-Wargument-mismatch]

genmap.f:3218:72:

call copy (zc,buf(34),8) !34--49

1

Warning: Type mismatch in argument 'y' at (1); passed INTEGER(4) to REAL(8) [-Wargument-mismatch]

genmap.f:3220:72:

call copy (xc,buf( 2),4) !2 --9

1

Warning: Type mismatch in argument 'y' at (1); passed INTEGER(4) to REAL(8) [-Wargument-mismatch]

genmap.f:3221:72:

call copy (yc,buf(10),4) !10--17

1

Warning: Type mismatch in argument 'y' at (1); passed INTEGER(4) to REAL(8) [-Wargument-mismatch]

genmap.f:3226:72:

call copy4r(xc,buf( 1),8)

1

Warning: Type mismatch in argument 'b' at (1); passed INTEGER(4) to REAL(4) [-Wargument-mismatch]

genmap.f:3227:72:

call copy4r(yc,buf( 9),8)

1

Warning: Type mismatch in argument 'b' at (1); passed INTEGER(4) to REAL(4) [-Wargument-mismatch]

genmap.f:3228:72:

call copy4r(zc,buf(17),8)

1

Warning: Type mismatch in argument 'b' at (1); passed INTEGER(4) to REAL(4) [-Wargument-mismatch]

genmap.f:3230:72:

call copy4r(xc,buf( 1),4)

1

Warning: Type mismatch in argument 'b' at (1); passed INTEGER(4) to REAL(4) [-Wargument-mismatch]

genmap.f:3231:72:

call copy4r(yc,buf( 5),4)

1

Warning: Type mismatch in argument 'b' at (1); passed INTEGER(4) to REAL(4) [-Wargument-mismatch]

genmap.f:247:16:

$ ('Error reading ncurve in makemesh ',ierr)

1

Warning: Character length of actual argument shorter than of dummy argument 'name' (33/40) at (1) [-Wargument-mismatch]

genmap.f:251:16:

$ ('Error reading curve data in makemesh ',ierr)

1

Warning: Character length of actual argument shorter than of dummy argument 'name' (37/40) at (1) [-Wargument-mismatch]

genmap.f:257:16:

$ ('Error reading ncurve in makemesh ',ierr)

1

Warning: Character length of actual argument shorter than of dummy argument 'name' (33/40) at (1) [-Wargument-mismatch]

genmap.f:261:16:

$ ('Error reading curve data in makemesh ',ierr)

1

Warning: Character length of actual argument shorter than of dummy argument 'name' (37/40) at (1) [-Wargument-mismatch]

genmap.f:3133:21:

& ('Error reading byte bcs ',ierr)

1

Warning: Character length of actual argument shorter than of dummy argument 'name' (23/40) at (1) [-Wargument-mismatch]

genmap.f:3167:21:

call copyi4(e,buf(1),1) !1-2

1

Warning: Rank mismatch in argument 'a' at (1) (rank-1 and scalar) [-Wargument-mismatch]

genmap.f:3168:21:

call copyi4(f,buf(3),1) !3-4

1

Warning: Rank mismatch in argument 'a' at (1) (rank-1 and scalar) [-Wargument-mismatch]

genmap.f:3169:72:

call copy (bl(1,f,e),buf(5),5) !5--14

1

Warning: Type mismatch in argument 'y' at (1); passed INTEGER(4) to REAL(8) [-Wargument-mismatch]

genmap.f:3170:72:

call chcopy(cbl( f,e),buf(15),3)!15-16

1

Warning: Type mismatch in argument 'y' at (1); passed INTEGER(4) to CHARACTER(1) [-Wargument-mismatch]

genmap.f:3177:72:

call copy48r ( bl(1,f,e),buf(3),5)

1

Warning: Type mismatch in argument 'b' at (1); passed INTEGER(4) to REAL(4) [-Wargument-mismatch]

genmap.f:3178:72:

call chcopy (cbl( f,e),buf(8),3)

1

Warning: Type mismatch in argument 'y' at (1); passed INTEGER(4) to CHARACTER(1) [-Wargument-mismatch]

genmap.f:3144:21:

& ('Error reading byte bcs ',ierr)

1

Warning: Character length of actual argument shorter than of dummy argument 'name' (23/40) at (1) [-Wargument-mismatch]

genmap.f:278:24:

call rd_bc_bin(cbc,bc,nelv,nelt,ifbswap)

1

Error: Actual argument contains too few elements for dummy argument 'cbc' (18/2700000) at (1)

genmap.f:282:14:

$ ('Error closing file in makemesh ',ierr)

1

Warning: Character length of actual argument shorter than of dummy argument 'name' (31/40) at (1) [-Wargument-mismatch]

genmap.f:509:24:

call cscan(string,'BOUNDARY',8) ! for now, fluid only

1

Warning: Character length of actual argument shorter than of dummy argument 'ke' (8/80) at (1) [-Wargument-mismatch]

genmap.f:520:26:

if (indx1(string,'NO ',3).ne.0) then

1

Warning: Character length of actual argument shorter than of dummy argument 's2' (3/80) at (1) [-Wargument-mismatch]

genmap.f:522:30:

call cscan(string,'BOUNDARY',8) ! then, temp only

1

Warning: Character length of actual argument shorter than of dummy argument 'ke' (8/80) at (1) [-Wargument-mismatch]

genmap.f:2936:53:

call tuple_sort(dx(0,i),lda,ninseg(iseg),j1,1,ind,dxt) !key=j1

1

Warning: Rank mismatch in argument 'key' at (1) (rank-1 and scalar) [-Wargument-mismatch]

genmap.f:302:72:

call unique_vertex2(cell,dx,ndim,nelt,q,i_n,j_n,j_o,wk)

1

Warning: Type mismatch in argument 'ifseg' at (1); passed INTEGER(4) to LOGICAL(4) [-Wargument-mismatch]

genmap.f:1148:18:

do k=2,n

2

next = a(k)

1

Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)

genmap.f:1150:11:

genmap.f:1147:72:

do k=2,n

2

genmap.f:1150:11:

a(k) = rank

1

Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)

genmap.f:121:72:

$ (cell,nv,nelt,irnk,dx,ndim,cbc,bc,nfc,w14,w5)

1

Warning: Type mismatch in argument 'iper' at (1); passed REAL(8) to INTEGER(4) -Wargument-mismatch]

genmap.f:3720:19:

genmap.f:3718:72:

do e=1,nel

2

genmap.f:3720:19:

j1 = ic2c(e+1)-1

1

Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)

genmap.f:2535:72:

call sbisect (pmap,f,p2,w,n)

1

Warning: Type mismatch in argument 'p' at (1); passed REAL(8) to INTEGER(4) [-Wargument-mismatch]

genmap.f:2861:17:

do i=2,n

2

s = s+x(i)*y(i)

1

Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)

genmap.f:2861:22:

do i=2,n

2

s = s+x(i)*y(i)

1

Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)

genmap.f:2629:21:

call ax(w,p,ia,ja,va,n)

1

Error: Actual argument contains too few elements for dummy argument 'ia' (1/2) at (1)

genmap.f:2554:30:

call lanczos2(f,rr,n,ev,d,u,niter)

1

Warning: Rank mismatch in argument 'ev' at (1) (rank-2 and scalar) [-Wargument-mismatch]

genmap.f:2559:72:

call sbisect (pmap,f,p2,w,n)

1

Warning: Type mismatch in argument 'p' at (1); passed REAL(8) to INTEGER(4) [-Wargument-mismatch]

genmap.f:3956:46:

$ ,nel,d,u,r,p2,w,rr,ev,m,ndim)

1

Warning: Rank mismatch in argument 'ev' at (1) (scalar and rank-1) [-Wargument-mismatch]

genmap.f:1419:72:

call icadd(pmap,p,nel)

1

Warning: Type mismatch in argument 'c' at (1); passed REAL(8) to INTEGER(4) [-Wargument-mismatch]

genmap.f:1202:72:

$ (n1,n2,pmap(j0),order,mo,elist(j0),n,cell,nv,p,w1,w2,w3)

1

Warning: Type mismatch in argument 'p' at (1); passed INTEGER(4) to REAL(8) [-Wargument-mismatch]

genmap.f:126:72:

$ ,w1,w2,w3,w4,w5)

1

Warning: Type mismatch in argument 'w3' at (1); passed REAL(8) to INTEGER(4) [-Wargument-mismatch]

genmap.f:147:72:

$ ,w1,w2,w3,w4,w5)

1

Warning: Type mismatch in argument 'w3' at (1); passed REAL(8) to INTEGER(4) [-Wargument-mismatch]

genmap.f:1102:27:

call isort(ja(j0),ind,nj)

1

Warning: Rank mismatch in argument 'ind' at (1) (rank-1 and scalar) [-Wargument-mismatch]

genmap.f:3536:30:

call breadth_first_fill(pb,pmax)

1

Error: Actual argument contains too few elements for dummy argument 'p' (1/2) at (1)

make[1]: *** [genmap.o] Error 1

ERROR: genmap failed to compile!

make: *** [all] Error 1

[robertwatkinssteeleii][~/Nek5000/tools]> ./maketools all

----------------------

Make amg_hypre...

----------------------

checking build system type... x86_64-apple-darwin18.6.0

checking host system type... x86_64-apple-darwin18.6.0

checking whether make sets $(MAKE)... yes

checking for ranlib... ranlib

checking for gcc... /opt/moose/mpich-3.3/clang-8.0.0/bin/mpicc

checking whether the C compiler works... yes

checking for C compiler default output file name... a.out

checking for suffix of executables...

checking whether we are cross compiling... configure: error: in `/Users/robertwatkinssteeleii/Nek5000/tools/amg_hypre/hypre/hypre-2.11.2/src':

configure: error: cannot run C compiled programs.

If you meant to cross compile, use `--host'.

See `config.log' for more details

make[1]: *** [lib] Error 1

ERROR: amg_hypre failed to compile!

make: *** [all] Error 1

Lane Carasik

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Jun 20, 2019, 6:29:33 PM6/20/19

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Can you look and see what the build.log file says in the genmap folder and copy that here or attach the file?

It should be nek5000/tools/genmap/build.log.

YuHsiang Lan

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Jun 20, 2019, 6:44:06 PM6/20/19

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What compiler and what version of compiler are you using?

I saw the same type of error if using gcc8 without -std=legacy

This issue should be fixed in the latest repo version of Nek5000.

Yu-Hsiang

--

Robert Steele II

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Jun 20, 2019, 6:48:24 PM6/20/19

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I'm not showing a build.log file under genmap:

robertwatkinssteeleii][~/Nek5000/tools/genmap]> ls

SIZE genmap.f makefile

Robert Steele II

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Jun 20, 2019, 6:51:37 PM6/20/19

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I'm using 8.3.0

YuHsiang Lan

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Jun 21, 2019, 8:26:16 AM6/21/19

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Hi Robert,

I assume you are using the tools from Nek5000 v17.

And, I can reproduce the same error using gcc8.2.1 on that.

This issues is fixed at the later version of Nek5000.

If you want to keep this version, I suggest you add "FFLAGS+=-std=legacy" into "tools/genmap/makefile"

Further info can refer to here:

https://github.com/Nek5000/Nek5000/issues/563

Yu-Hsiang

--

Robert Steele II

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Jun 21, 2019, 10:18:47 AM6/21/19

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Yu-Hsiang,

I downloaded v19 and tried it again with a similar error, so I added the line you suggested below into tools/genmap/makefile. Now I'm getting a fatal error that 'stdio.h' is not found. Any thoughts as to why the code can no longer find stdio.h? Doesn't that basically mean it can no longer find C?

Thanks.

Stefan Kerkemeier

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Jun 21, 2019, 10:32:08 AM6/21/19

to Robert Steele II, Nek5000

Please checkout the latest master on GitHub and try again. It should work out of the box without any modifications. Just tested it with the latest GNU compilers (v9.1) and it works for me.

-----Original message-----
> From:Robert Steele II <stee...@isu.edu>
> Sent: Friday 21st June 2019 17:18
> To: Nek5000 <nek...@googlegroups.com>
> Subject: [nek5000] Re: Maketools Error
>
> Yu-Hsiang,
>

> I downloaded v19 and tried it again with a similar error, so I added the line you suggested below into tools/genmap/makefile. Now Im getting a fatal error that stdio.h is not found. Any thoughts as to why the code can no longer find stdio.h? Doesnt that basically mean it can no longer find C?

>
> Thanks.
>
> On Friday, June 21, 2019 at 6:26:16 AM UTC-6, YuHsiang Lan wrote:
> Hi Robert,
>
> I assume you are using the tools from Nek5000 v17.
> And, I can reproduce the same error using gcc8.2.1 on that.
>
> This issues is fixed at the later version of Nek5000.
> If you want to keep this version, I suggest you add "FFLAGS+=-std=legacy" into "tools/genmap/makefile"
>
> Further info can refer to here:

> https://github.com/Nek5000/Nek5000/issues/563 <https://github.com/Nek5000/Nek5000/issues/563>

> Yu-Hsiang
> --
>
>
>
> On Thursday, June 20, 2019 at 5:51:37 PM UTC-5, Robert Steele II wrote:

> Im using 8.3.0

>
> On Thursday, June 20, 2019 at 4:44:06 PM UTC-6, YuHsiang Lan wrote:
> What compiler and what version of compiler are you using?
>
> I saw the same type of error if using gcc8 without -std=legacy
>
> This issue should be fixed in the latest repo version of Nek5000.
>
> Yu-Hsiang
> --
>
> On Thursday, June 20, 2019 at 5:21:55 PM UTC-5, Robert Steele II wrote:
> Hello Everyone,
>

> I am new to using Nek5000 and Im trying to mount the program onto an Apple I received. I get many errors and warnings when I try to compile genmap (per the Quickstart instructions), and also get an error which may or may not be related when I attempt to ./maketools all in the /tools folder. My error messages are listed below. Any help would be appreciated. Thanks!

>
> Rob
>
> [robertwatkinssteeleii][~/Nek5000/tools]> ./maketools genmap
> ----------------------
> Make genmap...
> ----------------------
> /opt/moose/mpich-3.3/clang-8.0.0/bin/mpif90 -c -DMAXNEL=150000 -cpp -fdefault-real-8 genmap.f
> genmap.f:886:18:
>

> len = indx1(prompt,$,1) - 1

> 1
> Warning: Rank mismatch in argument s1 at (1) (scalar and rank-1) [-Wargument-mismatch]
> genmap.f:220:24:
>
> call linearmsh(cell,nelv,nelt,ndim)
> 1
> Error: Actual argument contains too few elements for dummy argument cell (1/2) at (1)
> genmap.f:375:27:
>

> call cscan(string,MESH DATA,9)

> 1
> Warning: Character length of actual argument shorter than of dummy argument ke (9/80) at (1) [-Wargument-mismatch]
> genmap.f:3292:9:
>

> $ (Error opening file in open_bin_file ,ierr)

> 1
> Warning: Character length of actual argument shorter than of dummy argument name (36/40) at (1) [-Wargument-mismatch]
> genmap.f:3295:9:
>

> $ (Error reading header in open_bin_file ,ierr)

> 1
> Warning: Character length of actual argument shorter than of dummy argument name (38/40) at (1) [-Wargument-mismatch]
> genmap.f:3211:10:
>

> $ (Error byte_reverse in buf_to_xy ,ierr)

> $ (Error reading ncurve in makemesh ,ierr)

> 1
> Warning: Character length of actual argument shorter than of dummy argument name (33/40) at (1) [-Wargument-mismatch]
> genmap.f:251:16:
>

> $ (Error reading curve data in makemesh ,ierr)

> 1
> Warning: Character length of actual argument shorter than of dummy argument name (37/40) at (1) [-Wargument-mismatch]
> genmap.f:257:16:
>

> $ (Error reading ncurve in makemesh ,ierr)

> 1
> Warning: Character length of actual argument shorter than of dummy argument name (33/40) at (1) [-Wargument-mismatch]
> genmap.f:261:16:
>

> $ (Error reading curve data in makemesh ,ierr)

> 1
> Warning: Character length of actual argument shorter than of dummy argument name (37/40) at (1) [-Wargument-mismatch]
> genmap.f:3133:21:
>

> & (Error reading byte bcs ,ierr)

> 1
> Warning: Character length of actual argument shorter than of dummy argument name (23/40) at (1) [-Wargument-mismatch]
> genmap.f:278:24:
>
> call rd_bc_bin(cbc,bc,nelv,nelt,ifbswap)
> 1
> Error: Actual argument contains too few elements for dummy argument cbc (18/2700000) at (1)
> genmap.f:282:14:
>

> $ (Error closing file in makemesh ,ierr)

> 1
> Warning: Character length of actual argument shorter than of dummy argument name (31/40) at (1) [-Wargument-mismatch]
> genmap.f:509:24:
>

> call cscan(string,BOUNDARY,8) ! for now, fluid only

> 1
> Warning: Character length of actual argument shorter than of dummy argument ke (8/80) at (1) [-Wargument-mismatch]
> genmap.f:520:26:
>

> if (indx1(string,NO ,3).ne.0) then

> 1
> Warning: Character length of actual argument shorter than of dummy argument s2 (3/80) at (1) [-Wargument-mismatch]
> genmap.f:522:30:
>

> call cscan(string,BOUNDARY,8) ! then, temp only

> If you meant to cross compile, use `--host.

> See `config.log for more details
> make[1]: *** [lib] Error 1
>
> ERROR: amg_hypre failed to compile!
> make: *** [all] Error 1

> --
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Robert Steele II

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Jun 21, 2019, 10:58:06 AM6/21/19

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Stefan,

I downloaded the latest master from GitHub and only changed the name from Nek5000-master to Nek5000, then ran the following:

[robertwatkinssteeleii][~]> cd ~/Nek5000/tools; ./maketools genmap

building genmap ... failed

FATAL ERROR occured during compilation!

Check build.log for details

Attached is the build.log rtf file.

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build.log.rtf

Robert Steele II

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Jun 21, 2019, 11:04:14 AM6/21/19

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Sorry the rtf file didn't have all of the build.log. Here is just the build.log file

On Friday, June 21, 2019 at 8:32:08 AM UTC-6, StefanK wrote:

> To unsubscribe from this group and stop receiving emails from it, send an email to nek5000+unsubscribe@googlegroups.com <mailto:nek5000+unsubscribe@googlegroups.com>.
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build.log

Robert Steele II

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Jun 21, 2019, 4:24:31 PM6/21/19

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I was eventually able to get maketools work by uncommenting GCC and FCC in the maketools file. Now I'm getting a similar error while running makenek:

[robertwatkinssteeleii][~/Nek5000/run/eddy_uv]> makenek eddy_uv

using source path: /Users/robertwatkinssteeleii/Nek5000

generating makefile ... done

building 3rd-party dependencies ...

An ERROR occured, see build.log for details

The build.log is attached, but in a nutshell the program is not seeing stdlib.h or stdio.h.

Things I've tried to correct:

- Uncomment GCC and FCC in the makenek file (in /bin)

- Run makenek clean and clear 3rd party dependencies

- Rerun makenek eddy_uv with the same error.

build.log

YuHsiang Lan

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Jun 21, 2019, 4:38:08 PM6/21/19

to Nek5000

Hi Robert,

I might be wrong, but it might be your compiler is not installed properly.

When you said uncommenting GCC and FC, did you mean you compile with gcc and gfortran instead of mpicc for genmap? what's your build.log said about the compiler for gnemap?

I guess your mpicc is not working...

Can you do mpicc -v and gcc -v to see if they are the same?

Yu-Hsiang

--

Robert Steele II

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Jun 21, 2019, 4:48:18 PM6/21/19

to Nek5000

I think you may be right.

Here's what I get:

[robertwatkinssteeleii][~/Nek5000/run/eddy_uv]> mpicc -v

mpicc for MPICH version 3.3

clang version 8.0.0 (tags/RELEASE_800/final)

Target: x86_64-apple-darwin18.6.0

Thread model: posix

InstalledDir: /opt/moose/llvm-8.0.0/bin

clang-8: warning: argument unused during compilation: '-I /opt/moose/mpich-3.3/clang-8.0.0/include' [-Wunused-command-line-argument]

and

[robertwatkinssteeleii][~/Nek5000/run/eddy_uv]> gcc -v

Using built-in specs.

COLLECT_GCC=gcc

COLLECT_LTO_WRAPPER=/opt/moose/gcc-8.3.0/libexec/gcc/x86_64-apple-darwin18.5.0/8.3.0/lto-wrapper

Target: x86_64-apple-darwin18.5.0

Configured with: ../gcc-8.3.0/configure --prefix=/opt/moose/gcc-8.3.0 --disable-multilib --enable-languages=c,c++,fortran,jit --enable-checking=release --enable-host-shared --with-pic --with-system-zlib --disable-nls --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

Thread model: posix

gcc version 8.3.0 (GCC)

However when I check gcc via Homebrew, it say I have 9.1, so I'm not really sure what's going on (to be honest I was issued this Mac a few days ago by INL, and I don't know what black magic they put in it before I got it).

Any suggestions? I got genmap to work fine, so I'm not entirely sure why makenek is acting up now.

YuHsiang Lan

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Jun 21, 2019, 5:09:39 PM6/21/19

to Nek5000

Hi Robert,

I'm not familiar to clang compiler, so I can't help you compile Nek5000 with it.

But I suggest you compile Nek5000 with gcc and gfortran.

I'm using linux, and I can configure the "alternatives" with this command "sudo galternatives"

You can also try

sudo update-alternatives --config <options>

options:

cc

c++

f77

mpirun

mpi

Or, reinstall gcc mpich may be a easier options

Hope this help,

Yu-Hsiang

--

Stefan Kerkemeier

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Jun 21, 2019, 5:34:54 PM6/21/19

to Robert Steele II, Nek5000

Can you also run and post the output of:

mpif77 -show
mpicc -show

-----Original message-----
> From:Robert Steele II <stee...@isu.edu>
> Sent: Friday 21st June 2019 23:48
> To: Nek5000 <nek...@googlegroups.com>
> Subject: Re: [nek5000] Re: Maketools Error
>
> I think you may be right.

> Heres what I get:

>
> [robertwatkinssteeleii][~/Nek5000/run/eddy_uv]> mpicc -v
> mpicc for MPICH version 3.3
> clang version 8.0.0 (tags/RELEASE_800/final)
> Target: x86_64-apple-darwin18.6.0
> Thread model: posix
> InstalledDir: /opt/moose/llvm-8.0.0/bin
> clang-8: warning: argument unused during compilation: -I /opt/moose/mpich-3.3/clang-8.0.0/include [-Wunused-command-line-argument]
>
> and
>
> [robertwatkinssteeleii][~/Nek5000/run/eddy_uv]> gcc -v
> Using built-in specs.
> COLLECT_GCC=gcc
> COLLECT_LTO_WRAPPER=/opt/moose/gcc-8.3.0/libexec/gcc/x86_64-apple-darwin18.5.0/8.3.0/lto-wrapper
> Target: x86_64-apple-darwin18.5.0
> Configured with: ../gcc-8.3.0/configure --prefix=/opt/moose/gcc-8.3.0 --disable-multilib --enable-languages=c,c++,fortran,jit --enable-checking=release --enable-host-shared --with-pic --with-system-zlib --disable-nls --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> Thread model: posix
> gcc version 8.3.0 (GCC)
>

> However when I check gcc via Homebrew, it say I have 9.1, so Im not really sure whats going on (to be honest I was issued this Mac a few days ago by INL, and I dont know what black magic they put in it before I got it).
>
> Any suggestions? I got genmap to work fine, so Im not entirely sure why makenek is acting up now.

>
> On Friday, June 21, 2019 at 2:38:08 PM UTC-6, YuHsiang Lan wrote:
> Hi Robert,
>
> I might be wrong, but it might be your compiler is not installed properly.
>

> When you said uncommenting GCC and FC, did you mean you compile with gcc and gfortran instead of mpicc for genmap? whats your build.log said about the compiler for gnemap?

>
> I guess your mpicc is not working...
> Can you do mpicc -v and gcc -v to see if they are the same?
>
> Yu-Hsiang
> --
>
>
> On Friday, June 21, 2019 at 3:24:31 PM UTC-5, Robert Steele II wrote:

> I was eventually able to get maketools work by uncommenting GCC and FCC in the maketools file. Now Im getting a similar error while running makenek:

>
> [robertwatkinssteeleii][~/Nek5000/run/eddy_uv]> makenek eddy_uv
> using source path: /Users/robertwatkinssteeleii/Nek5000
> generating makefile ... done
> building 3rd-party dependencies ...
> An ERROR occured, see build.log for details
>
> The build.log is attached, but in a nutshell the program is not seeing stdlib.h or stdio.h.
>

> Things Ive tried to correct:

>
> - Uncomment GCC and FCC in the makenek file (in /bin)
> - Run makenek clean and clear 3rd party dependencies
> - Rerun makenek eddy_uv with the same error.
>
>
> On Friday, June 21, 2019 at 9:04:14 AM UTC-6, Robert Steele II wrote:

> Sorry the rtf file didnt have all of the build.log. Here is just the build.log file

>
> On Friday, June 21, 2019 at 8:32:08 AM UTC-6, StefanK wrote:Please checkout the latest master on GitHub and try again. It should work out of the box without any modifications. Just tested it with the latest GNU compilers (v9.1) and it works for me.
>
>
> -----Original message-----
>

> > From:Robert Steele II <stee...@isu.edu <mailto:stee...@isu.edu>>
>
> > Sent: Friday 21st June 2019 17:18
>

> > To: Nek5000 <nek...@googlegroups.com <mailto:nek...@googlegroups.com>>

>
> > Subject: [nek5000] Re: Maketools Error
>
> >
>
> > Yu-Hsiang,
>
> >
>
> > I downloaded v19 and tried it again with a similar error, so I added the line you suggested below into tools/genmap/makefile. Now Im getting a fatal error that stdio.h is not found. Any thoughts as to why the code can no longer find stdio.h? Doesnt that basically mean it can no longer find C?
>
> >
>
> > Thanks.
>
> >
>
> > On Friday, June 21, 2019 at 6:26:16 AM UTC-6, YuHsiang Lan wrote:
>
> > Hi Robert,
>
> >
>
> > I assume you are using the tools from Nek5000 v17.
>
> > And, I can reproduce the same error using gcc8.2.1 on that.
>
> >
>
> > This issues is fixed at the later version of Nek5000.
>
> > If you want to keep this version, I suggest you add "FFLAGS+=-std=legacy" into "tools/genmap/makefile"
>
> >
>
> > Further info can refer to here:
>

> > https://github.com/Nek5000/Nek5000/issues/563 <https://github.com/Nek5000/Nek5000/issues/563> <https://github.com/Nek5000/Nek5000/issues/563 <https://github.com/Nek5000/Nek5000/issues/563>>

>
>
> --
> You received this message because you are subscribed to the Google Groups "Nek5000" group.

> To unsubscribe from this group and stop receiving emails from it, send an email to nek5000+u...@googlegroups.com <mailto:nek5000+u...@googlegroups.com>.
> To post to this group, send email to nek...@googlegroups.com <mailto:nek...@googlegroups.com>.

> Visit this group at https://groups.google.com/group/nek5000 <https://groups.google.com/group/nek5000>.

> To view this discussion on the web visit https://groups.google.com/d/msgid/nek5000/4e22673c-6ced-4c88-9bea-b4d722150e0a%40googlegroups.com <https://groups.google.com/d/msgid/nek5000/4e22673c-6ced-4c88-9bea-b4d722150e0a%40googlegroups.com?utm_medium=email&utm_source=footer>.

Robert Steele II

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Jun 21, 2019, 6:35:02 PM6/21/19

to Nek5000

Here's what I get from those:

[robertwatkinssteeleii][~]> mpif77 -show

gfortran -Wl,-commons,use_dylibs -I/opt/moose/mpich-3.3/clang-8.0.0/include -I/opt/moose/mpich-3.3/clang-8.0.0/include -L/opt/moose/mpich-3.3/clang-8.0.0/lib -lmpifort -lmpi -lpmpi

[robertwatkinssteeleii][~]> mpicc -show

clang -Wl,-commons,use_dylibs -I/opt/moose/mpich-3.3/clang-8.0.0/include -L/opt/moose/mpich-3.3/clang-8.0.0/lib -lmpi -lpmpi

[robertwatkinssteeleii][~]>

> > To: Nek5000 <nek...@googlegroups.com <mailto:nek5000@googlegroups.com>>

> > To unsubscribe from this group and stop receiving emails from it, send an email to nek5000+unsubscribe@googlegroups.com <mailto:nek5000%2Bunsubscribe@googlegroups.com> <mailto:nek5000+unsubscribe@googlegroups.com <mailto:nek5000%2Bunsubscribe@googlegroups.com>>.
>
> > To post to this group, send email to nek...@googlegroups.com <mailto:nek5000@googlegroups.com> <mailto:nek5000@googlegroups.com <mailto:nek5000@googlegroups.com>>.

>
> > Visit this group at https://groups.google.com/group/nek5000 <https://groups.google.com/group/nek5000> <https://groups.google.com/group/nek5000 <https://groups.google.com/group/nek5000>>.
>
> > To view this discussion on the web visit https://groups.google.com/d/msgid/nek5000/fd92c6b2-a613-4832-90b1-499f5e2ccdec%40googlegroups.com <https://groups.google.com/d/msgid/nek5000/fd92c6b2-a613-4832-90b1-499f5e2ccdec%40googlegroups.com> <https://groups.google.com/d/msgid/nek5000/fd92c6b2-a613-4832-90b1-499f5e2ccdec%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/nek5000/fd92c6b2-a613-4832-90b1-499f5e2ccdec%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
> > For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout> <https://groups.google.com/d/optout <https://groups.google.com/d/optout>>.
>
>
> --
> You received this message because you are subscribed to the Google Groups "Nek5000" group.

> To unsubscribe from this group and stop receiving emails from it, send an email to nek5000+unsubscribe@googlegroups.com <mailto:nek5000+unsubscribe@googlegroups.com>.
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Stefan Kerkemeier

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Jun 21, 2019, 6:41:03 PM6/21/19

to Robert Steele II, Nek5000

The C compiler (clang) you're using is not supported. I usually install gcc + openmpi using homebrew on OSX.

-----Original message-----
> From:Robert Steele II <stee...@isu.edu>
> Sent: Saturday 22nd June 2019 1:35
> To: Nek5000 <nek...@googlegroups.com>
> Subject: Re: [nek5000] Re: Maketools Error
>
>

> Heres what I get from those:

>
> [robertwatkinssteeleii][~]> mpif77 -show
> gfortran -Wl,-commons,use_dylibs -I/opt/moose/mpich-3.3/clang-8.0.0/include -I/opt/moose/mpich-3.3/clang-8.0.0/include -L/opt/moose/mpich-3.3/clang-8.0.0/lib -lmpifort -lmpi -lpmpi
> [robertwatkinssteeleii][~]> mpicc -show
> clang -Wl,-commons,use_dylibs -I/opt/moose/mpich-3.3/clang-8.0.0/include -L/opt/moose/mpich-3.3/clang-8.0.0/lib -lmpi -lpmpi
> [robertwatkinssteeleii][~]>
>
> On Friday, June 21, 2019 at 3:34:54 PM UTC-6, StefanK wrote:Can you also run and post the output of:
>
>
> mpif77 -show
>
> mpicc -show
>
>
> -----Original message-----
>

> > From:Robert Steele II <stee...@isu.edu <mailto:stee...@isu.edu>>
>

> > Sent: Friday 21st June 2019 23:48
>

> > To: Nek5000 <nek...@googlegroups.com <mailto:nek...@googlegroups.com>>

> > > To: Nek5000 <nek...@googlegroups.com <mailto:nek...@googlegroups.com> <mailto:nek...@googlegroups.com <mailto:nek...@googlegroups.com>>>

>
> >
>
> > > Subject: [nek5000] Re: Maketools Error
>
> >
>
> > >
>
> >
>
> > > Yu-Hsiang,
>
> >
>
> > >
>
> >
>
> > > I downloaded v19 and tried it again with a similar error, so I added the line you suggested below into tools/genmap/makefile. Now Im getting a fatal error that stdio.h is not found. Any thoughts as to why the code can no longer find stdio.h? Doesnt that basically mean it can no longer find C?
>
> >
>
> > >
>
> >
>
> > > Thanks.
>
> >
>
> > >
>
> >
>
> > > On Friday, June 21, 2019 at 6:26:16 AM UTC-6, YuHsiang Lan wrote:
>
> >
>
> > > Hi Robert,
>
> >
>
> > >
>
> >
>
> > > I assume you are using the tools from Nek5000 v17.
>
> >
>
> > > And, I can reproduce the same error using gcc8.2.1 on that.
>
> >
>
> > >
>
> >
>
> > > This issues is fixed at the later version of Nek5000.
>
> >
>
> > > If you want to keep this version, I suggest you add "FFLAGS+=-std=legacy" into "tools/genmap/makefile"
>
> >
>
> > >
>
> >
>
> > > Further info can refer to here:
>
> >
>

> > > https://github.com/Nek5000/Nek5000/issues/563 <https://github.com/Nek5000/Nek5000/issues/563> <https://github.com/Nek5000/Nek5000/issues/563 <https://github.com/Nek5000/Nek5000/issues/563>> <https://github.com/Nek5000/Nek5000/issues/563 <https://github.com/Nek5000/Nek5000/issues/563> <https://github.com/Nek5000/Nek5000/issues/563 <https://github.com/Nek5000/Nek5000/issues/563>>>

>
> >
>
> >
>
> > --
>
> > You received this message because you are subscribed to the Google Groups "Nek5000" group.
>

> > To unsubscribe from this group and stop receiving emails from it, send an email to nek5000+u...@googlegroups.com <mailto:nek5000%2Bunsu...@googlegroups.com> <mailto:nek5000+u...@googlegroups.com <mailto:nek5000%2Bunsu...@googlegroups.com>>.
>
> > To post to this group, send email to nek...@googlegroups.com <mailto:nek...@googlegroups.com> <mailto:nek...@googlegroups.com <mailto:nek...@googlegroups.com>>.

>
> > Visit this group at https://groups.google.com/group/nek5000 <https://groups.google.com/group/nek5000> <https://groups.google.com/group/nek5000 <https://groups.google.com/group/nek5000>>.
>

> > To view this discussion on the web visit https://groups.google.com/d/msgid/nek5000/4e22673c-6ced-4c88-9bea-b4d722150e0a%40googlegroups.com <https://groups.google.com/d/msgid/nek5000/4e22673c-6ced-4c88-9bea-b4d722150e0a%40googlegroups.com> <https://groups.google.com/d/msgid/nek5000/4e22673c-6ced-4c88-9bea-b4d722150e0a%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/nek5000/4e22673c-6ced-4c88-9bea-b4d722150e0a%40googlegroups.com?utm_medium=email&utm_source=footer>>.

>
> > For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout> <https://groups.google.com/d/optout <https://groups.google.com/d/optout>>.
>
>
> --
> You received this message because you are subscribed to the Google Groups "Nek5000" group.

> To unsubscribe from this group and stop receiving emails from it, send an email to nek5000+u...@googlegroups.com <mailto:nek5000+u...@googlegroups.com>.
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> Visit this group at https://groups.google.com/group/nek5000 <https://groups.google.com/group/nek5000>.

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