RESCU+ 1.1.0 installation

shwhyshwhy

I am trying to install RESCU+ 1.1.0. However, one of the dependency dftd3 cannot be installed properly using

bash install_dep.sh --library dftd3.sh  --buildpath /tmp --prefix $HOME/.local

The error log is:

--2022-09-16 17:57:20--  https://storage.googleapis.com/rescuplus-dependencies/dftd3-3.2.tar.gz
Resolving storage.googleapis.com (storage.googleapis.com)... 142.251.41.48, 142.251.33.176, 142.251.32.80, ...
Connecting to storage.googleapis.com (storage.googleapis.com)|142.251.41.48|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 555621 (543K) [application/gzip]
Saving to: ‘dftd3-3.2.tar.gz’

     0K .......... .......... .......... .......... ..........  9% 21.3M 0s
    50K .......... .......... .......... .......... .......... 18% 28.2M 0s
   100K .......... .......... .......... .......... .......... 27% 59.4M 0s
   150K .......... .......... .......... .......... .......... 36% 67.6M 0s
   200K .......... .......... .......... .......... .......... 46% 71.2M 0s
   250K .......... .......... .......... .......... .......... 55% 81.8M 0s
   300K .......... .......... .......... .......... .......... 64% 81.2M 0s
   350K .......... .......... .......... .......... .......... 73% 78.4M 0s
   400K .......... .......... .......... .......... .......... 82% 81.4M 0s
   450K .......... .......... .......... .......... .......... 92% 83.0M 0s
   500K .......... .......... .......... .......... ..        100% 94.8M=0.01s

2022-09-16 17:57:20 (54.6 MB/s) - ‘dftd3-3.2.tar.gz’ saved [555621/555621]

making dftd3.o from dftd3.f
gfortran -O3 -fPIC -c dftd3.f -o dftd3.o
dftd3.f:4065:72:

 4065 |    55 IF(N.EQ.ND .OR. N.EQ.NE)GOTO 57
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 55 at (1)
dftd3.f:4092:72:

 4092 |       if(m)10,10,80
      |                                                                        1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
dftd3.f:4111:72:

 4111 |    20 k2=k1+kk
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 20 at (1)
dftd3.f:4124:72:

 4124 |    30 k2=k2+kk
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 30 at (1)
dftd3.f:4125:72:

 4125 |    40 kd=kd+nkpb
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 40 at (1)
dftd3.f:4137:72:

 4137 |    60 k2=k1+kk
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 60 at (1)
dftd3.f:4150:72:

 4150 |       do 90 j=1,n
      |                                                                        1
Warning: Fortran 2018 deleted feature: Shared DO termination label 90 at (1)
dftd3.f:4153:72:

 4153 |    90 i2=i1+(nkpb-1)*n
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 90 at (1)
dftd3.f:7183:24:

 7183 |         subroutine split(str,delims,before,sep)
      |                        1
Warning: Interface mismatch in global procedure ‘split’ at (1): INTENT mismatch in argument 'sep' [-Wargument-mismatch]
dftd3.f:866:38:

  866 |             write(*,'("L"2i1,2E14.6)'),i,j,dum,g_lat(j,i)
      |                                      1
Warning: Legacy Extension: Comma before i/o item list at (1)
making copyc6.o from copyc6.f
gfortran -O3 -fPIC -c copyc6.f -o copyc6.o
gfortran -static dftd3.o copyc6.o    -o dftd3  
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
make: *** [dftd3] Error 1

Could you please give us some guidance on this? Thank you so much!

vincentm

Hi shwhyshwhy ,

It seems you are missing libc and the math libraries. Can you provide more info on your environment?

vincentm

shwhyshwhy bash install_dep.sh --library dftd3.sh --buildpath /tmp --prefix $HOME/.local

Dear @shwhyshwhy,

It should be --library dftd3, not --library dftd3.sh. Also, I can fix the script in the next release, but in the meantime, can you change this line

make FFLAGS="-O3 -fPIC" CCFLAGS="-O3 -fPIC" &>>${BUILDPATH}/logs/${LIB}.log

for

make FFLAGS="-O3 -fPIC" CCFLAGS="-O3 -fPIC" &>>${BUILDPATH}/logs/${LIB}.log || \
make LINKER="gfortran" FFLAGS="-O3 -fPIC" CCFLAGS="-O3 -fPIC" &>>${BUILDPATH}/logs/${LIB}.log

shwhyshwhy

Dear vincentm I have the following modules loaded on cluster Niagara:

module load gcc/9.4.0
module load openmpi/4.1.1
module load cmake/3.21.4
module load python/3.8.5
export PKG_CONFIG_PATH=/home/h/hongguo/syuan43/.local/lib/pkgconfig:$PKG_CONFIG_PATH
export PATH=$PATH:$HOME/.local/bin
export LD_LINK_PATH=$HOME/.local/lib

Thank you very much!

Kan

vincentm I had the same problem on installing the RESCU+ 1.1.0.rc, and looking forward to finding a solution.

Kan

vincentm I've tried to fix the dftd3.sh, but the error remained the same.

vincentm

The error will still show in the log, but the binary should be built by the second command. Can you see dftd3 in your path in the end?

Kan

vincentm Yes, the dftd3 could be created in the bin file folder, but still have problem in the following installation of "PREFIX=/path/to/install make configure".

nanoadmin

Kan

I was able to reproduce the error on niagara. It seems to be caused by the gcc module not including the libraries to statically link the executable (https://stackoverflow.com/questions/16024978/usr-bin-ld-cannot-find-lc-while-compiling-with-makefile). I couldn't find a way to load the libraries but removing the -static from the linker flags seems to resolve the issue and should not cause any problems.

Make sure to have the modules you specified loaded. Either run the following commands or copy this into a .sh file and run it (do not use the install_dep scripts). Make sure PREFIX is set to the same prefix you will be using for the dependencies.

set -x
PREFIX="${PREFIX:-$HOME/.local/nanoacademic}"

#download dftd3
wget https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3/dftd3.tgz
mkdir dftd3
tar -xf dftd3.tgz --directory dftd3
cd dftd3

#fix static linking
sed -i 's/LINKER = gfortran -static/LINKER = gfortran/g' Makefile
make

#install
mkdir -p $PREFIX/bin
cp dftd3 $PREFIX/bin/

If the script run succesfully you can delete the dftd3.tgz and the dftd3 directory.

Let me know if this works.

Guillaume

Kan

nanoadmin Thanks for your reply. The script works, but the installation make build also showed some error.

[388/976] Linking target src/rescuplus_license
FAILED: src/rescuplus_license
mpicxx  -o src/rescuplus_license src/rescuplus_license.p/c50ca51135b912dc6d3c508bb6db6e3.f08.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 '-Wl,-rpath,$ORIGIN/:$ORIGIN/../../subprojects/ilasmat:$ORIGIN/../../subprojects/nanolic:$ORIGIN/../subprojects/besselj:/home/h/hongguo/kan/.local/dependence/1.1.0/lib' -Wl,-rpath-link,/gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0-rc1/build/src -Wl,-rpath-link,/home/h/hongguo/kan/.local/dependence/1.1.0/lib -Wl,-rpath-link,/gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0-rc1/build/../subprojects/ilasmat -Wl,-rpath-link,/gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0-rc1/build/../subprojects/nanolic -Wl,-rpath-link,/gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0-rc1/build/subprojects/besselj -Wl,--start-group src/liblic.so src/libkinds.so src/libio.so src/libarrayutils.so src/libwblas.so src/libmatutils.so src/libwmpi.so /gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0-rc1/subprojects/ilasmat/ILasMatInterface.so /gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0-rc1/subprojects/nanolic/libnanolic-linux-amd64.so -Wl,-rpath -Wl,/scinet/niagara/software/2019b/opt/gcc-9.4.0/openmpi/4.1.1/lib -Wl,--enable-new-dtags /scinet/niagara/software/2019b/opt/gcc-9.4.0/openmpi/4.1.1/lib/libmpi_usempif08.so /scinet/niagara/software/2019b/opt/gcc-9.4.0/openmpi/4.1.1/lib/libmpi_usempi_ignore_tkr.so /scinet/niagara/software/2019b/opt/gcc-9.4.0/openmpi/4.1.1/lib/libmpi_mpifh.so /scinet/niagara/software/2019b/opt/gcc-9.4.0/openmpi/4.1.1/lib/libmpi.so -lgfortran -lm -Wl,--end-group
/gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0-rc1/subprojects/nanolic/libnanolic-linux-amd64.so: undefined reference to `log@GLIBC_2.29'
/gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0-rc1/subprojects/nanolic/libnanolic-linux-amd64.so: undefined reference to `pow@GLIBC_2.29'
collect2: error: ld returned 1 exit status
[403/976] Compiling Fortran object test/unit/c30f14922b2135d70addf5ecc...cu_rescuplus-1.1.0-rc1_test_unit_c30f14922b2135d70addf5eccb8adb3.f08.o
ninja: build stopped: subcommand failed.
make: *** [Makefile:42: build] Error 1

It seems like the license error.

Kan

nanoadmin Hi. I've tried to install the rescuplus-1.1.0 version on niagara. The dftd3 problem has solved, but the installation still showed some error when executing the command make build.

[975/985] Linking target src/rescuplus
FAILED: src/rescuplus
mpifort -o src/rescuplus src/rescuplus.p/cdd9661435d2f04f80a05782495179d.f90.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 '-Wl,-rpath,$ORIGIN/:$ORIGIN/../../subprojects/nanolic:$ORIGIN/../subprojects/besselj:/home/h/hongguo/kan/.local/dependence/1.1.0/lib' -Wl,-rpath-link,/gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0/build/src -Wl,-rpath-link,/home/h/hongguo/kan/.local/dependence/1.1.0/lib -Wl,-rpath-link,/gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0/build/../subprojects/nanolic -Wl,-rpath-link,/gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0/build/subprojects/besselj -Wl,--start-group src/liblic.so src/libkinds.so src/libio.so src/libarrayutils.so src/libwblas.so src/libmatutils.so src/libwmpi.so src/libdistarray.so src/libwhdf5.so src/libmpidist.so src/libwfftw.so src/libcell.so src/libgridFunc.so src/libpoisson.so src/libdft.so src/libatoms.so src/libwscalapack.so src/libaomat.so src/libpwMod.so src/libatomsys.so src/libsolver.so src/libbasicplus_calc.so src/librescuplus_calc.so /home/h/hongguo/kan/.local/dependence/1.1.0/lib/libjsonfortran.so -Wl,-rpath -Wl,/scinet/niagara/software/2019b/opt/gcc-9.4.0/openmpi/4.1.1/lib -Wl,--enable-new-dtags /scinet/niagara/software/2019b/opt/gcc-9.4.0/openmpi/4.1.1/lib/libmpi_usempif08.so /scinet/niagara/software/2019b/opt/gcc-9.4.0/openmpi/4.1.1/lib/libmpi_usempi_ignore_tkr.so /scinet/niagara/software/2019b/opt/gcc-9.4.0/openmpi/4.1.1/lib/libmpi_mpifh.so /scinet/niagara/software/2019b/opt/gcc-9.4.0/openmpi/4.1.1/lib/libmpi.so -Wl,--end-group
/gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0/build/../subprojects/nanolic/libnanolic-linux-amd64.so: undefined reference to log@GLIBC_2.29' /gpfs/fs0/project/h/hongguo/kan/rescu/rescuplus-1.1.0/build/../subprojects/nanolic/libnanolic-linux-amd64.so: undefined reference topow@GLIBC_2.29'
collect2: error: ld returned 1 exit status
[978/985] Compiling Fortran object src/libdcal_calc.so.p/_gpfs_fs0_pro...uo_kan_rescu_rescuplus-1.1.0_src_ce398d2ed482eb3197675d33411b3d8.f90.o
ninja: build stopped: subcommand failed.
make: *** [Makefile:42: build] Error 1

vincentm

Hi @Kan ,
There is currently an issue with floating license on Niagara. Since you are part of the hongguo group, I'll message you in private to grant you access to his installation.

For the record, I installed rescu+-1.1.0 with the following env on Niagara

module purge
module load CCEnv StdEnv/2020
module load gcc/9.3.0 openmpi/4.0.3 python/3.8
module rm imkl

Kan

vincentm 😀 OK. Thanks a lot.