error on mac, no crash

[DaniBodor]

@gcroci2 tested the scripts on her system and got an error regarding line 157 of the .sh script. Something about -n not being defined. The script still seems to have finished without problems.
This doesn't happen on my system, possibly because she uses a mac and I run ubuntu.

[joaomcteixeira]

Hi @DaniBodor

I am using the following bash and ubuntu:

· bash --version
GNU bash, version 5.1.16(1)-release (x86_64-pc-linux-gnu)

· lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 22.04.2 LTS
Release:	22.04
Codename:	jammy

I don't have access to a MAC to test. If the error says -n is not defined may be the script used one single core. Try to define -n. Can you paste the full error? Best,

[gcroci2]

If I run

pdb_prepare.sh pdblist 1

or

pdb_prepare.sh pdblist

It gives me

performing with 1 CPUS..
processing 1ATN_3w...
/Users/giuliacrocioni/Desktop/docs/eScience/projects/pdbprep/pdb_prepare.sh: line 157: wait: -n: invalid option
wait: usage: wait [n]

I just noticed that if I increase n (>1) then it works. Shouldn't work with only 1 cpu as well, though?

[joaomcteixeira]

Ah! I see. It will work with one CPU if you don't provide -n. But if you write -n, then it expects a number after it, -n 1, or -n N where N is the number.

[gcroci2]

Ah! I see. It will work with one CPU if you don't provide -n. But if you write -n, then it expects a number after it, -n 1, or -n N where N is the number.

Actually not, if I run pdb_prepare.sh pdblist it gives the same error as above

[DaniBodor]

@gcroci2 , if I saw correctly, it works either way, right? It just gives an error message, but does actually still process the data and outputs into folder 4, etc, right?

[joaomcteixeira]

| Actually not, if I run pdb_prepare.sh pdblist it gives the same error as above

I can't reproduce the error on my computer. Very likely a difference between the bash versions on Ubuntu and Mac. Sorry, I don't have access to any Mac to test it.

[gcroci2]

@gcroci2 , if I saw correctly, it works either way, right? It just gives an error message, but does actually still process the data and outputs into folder 4, etc, right?

exactly

[DaniBodor]

@joaomcteixeira , once you've made the newest changes, maybe @gcroci2 can test again and see if this is still an issue or not.

[joaomcteixeira]

Everything is done. @gcroci2 can you start from scratch to see if it works? The execution command is:

run_pdbprep.sh <PDBLIST> <N> where N is the number of cores you want to use. If you don't give N it will use only 1.

[gcroci2]

When I try to run run_pdbprep.sh pdblist, it gives me this error

(pdbprep) ➜  pdb_folder run_pdbprep.sh pdblist
ERROR: /home/user/PRAS does not exist or is not executable.

When I installed @joaomcteixeira's fork of Pras_Server, the last command (g++ -std=c++17 src/*.cpp -o PRAS) gave me these warnings:

warnings

src/CheckPDBatoms.cpp:611:2: warning: non-void function does not return a value in all control paths [-Wreturn-type]
        }
        ^
1 warning generated.
src/MissingHeavyAtoms.cpp:60:5: warning: non-void function does not return a value in all control paths [-Wreturn-type]
    }
    ^
1 warning generated.
src/PRAS.cpp:99:7: warning: left operand of comma operator has no effect [-Wunused-value]
        if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR;
             ^~~
src/PRAS.cpp:99:11: warning: left operand of comma operator has no effect [-Wunused-value]
        if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR;
                 ^~~~~
src/PRAS.cpp:99:17: warning: left operand of comma operator has no effect [-Wunused-value]
        if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR;
                       ^~~~~~~
src/PRAS.cpp:99:25: warning: left operand of comma operator has no effect [-Wunused-value]
        if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR;
                               ^~~~~~~~
src/PRAS.cpp:99:34: warning: left operand of comma operator has no effect [-Wunused-value]
        if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR;
                                        ^~~~~~
src/PRAS.cpp:99:41: warning: left operand of comma operator has no effect [-Wunused-value]
        if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR;
                                               ^~~~
src/PRAS.cpp:99:46: warning: left operand of comma operator has no effect [-Wunused-value]
        if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR;
                                                    ^~~~
7 warnings generated.
src/RepairPDB.cpp:30:3: warning: non-void function does not return a value in all control paths [-Wreturn-type]
  }
  ^
src/RepairPDB.cpp:38:3: warning: non-void function does not return a value in all control paths [-Wreturn-type]
  }
  ^
2 warnings generated.

[joaomcteixeira]

Hi Giulia, You need to update the Pras path on line 4 of the run_pdbprep.sh file. Maybe I should highlight that more on the installation instructions, sorry! Let me know if it works. Cheers, El mié., 20 sept. 2023 16:18, Giulia Crocioni ***@***.***> escribió:

…

When I try to run run_pdbprep.sh pdblist, it gives me this error (pdbprep) ➜ pdb_folder run_pdbprep.sh pdblist ERROR: /home/user/PRAS does not exist or is not executable. When I installed @joaomcteixeira <https://github.com/joaomcteixeira>'s fork of Pras_Server, the last command (g++ -std=c++17 src/*.cpp -o PRAS) gave me these warnings: warnings src/CheckPDBatoms.cpp:611:2: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 1 warning generated. src/MissingHeavyAtoms.cpp:60:5: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 1 warning generated. src/PRAS.cpp:99:7: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~ src/PRAS.cpp:99:11: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~~ src/PRAS.cpp:99:17: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~~~~ src/PRAS.cpp:99:25: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~~~~~ src/PRAS.cpp:99:34: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~~~ src/PRAS.cpp:99:41: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~ src/PRAS.cpp:99:46: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~ 7 warnings generated. src/RepairPDB.cpp:30:3: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ src/RepairPDB.cpp:38:3: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 2 warnings generated. — Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAWEOMRCCIA22QFWXCFCLHDX3L3MVANCNFSM6AAAAAAYT4HWUI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[gcroci2]

Hi Giulia, You need to update the Pras path on line 4 of the run_pdbprep.sh file. Maybe I should highlight that more on the installation instructions, sorry! Let me know if it works.

How should I update line 4?

Right now, installation instructions do not mention anything about updating the file, or am I wrong?

[joaomcteixeira]

Hi, On line 4 of the run_pdbprep.sh script there is the definition of the path of the Pras executable. The original script has a dummy path. You need to change that dummy path to the absolute path of the PRAS executable on your computer. Cheers and let me know, El lun., 25 sept. 2023 10:27, Giulia Crocioni ***@***.***> escribió:

…

Hi Giulia, You need to update the Pras path on line 4 of the run_pdbprep.sh file. Maybe I should highlight that more on the installation instructions, sorry! Let me know if it works. Cheers, El mié., 20 sept. 2023 16:18, Giulia Crocioni *@*. *> escribió: … <#m_-740801222133396838_> When I try to run run_pdbprep.sh pdblist, it gives me this error (pdbprep) ➜ pdb_folder run_pdbprep.sh pdblist ERROR: /home/user/PRAS does not exist or is not executable. When I installed @joaomcteixeira <https://github.com/joaomcteixeira> https://github.com/joaomcteixeira <https://github.com/joaomcteixeira>'s fork of Pras_Server, the last command (g++ -std=c++17 src/.cpp -o PRAS) gave me these warnings: warnings src/CheckPDBatoms.cpp:611:2: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 1 warning generated. src/MissingHeavyAtoms.cpp:60:5: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 1 warning generated. src/PRAS.cpp:99:7: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~ src/PRAS.cpp:99:11: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~~ src/PRAS.cpp:99:17: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~~~~ src/PRAS.cpp:99:25: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~~~~~ src/PRAS.cpp:99:34: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~~~ src/PRAS.cpp:99:41: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~ src/PRAS.cpp:99:46: warning: left operand of comma operator has no effect [-Wunused-value] if ((PDB,faspr,rotamer,mutation,ligand,addh,prot,ss).empty()) goto ERR; ^~~~ 7 warnings generated. src/RepairPDB.cpp:30:3: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ src/RepairPDB.cpp:38:3: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 2 warnings generated. — Reply to this email directly, view it on GitHub <#4 (comment) <#4 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAWEOMRCCIA22QFWXCFCLHDX3L3MVANCNFSM6AAAAAAYT4HWUI <https://github.com/notifications/unsubscribe-auth/AAWEOMRCCIA22QFWXCFCLHDX3L3MVANCNFSM6AAAAAAYT4HWUI> . You are receiving this because you were mentioned.Message ID: @.**> How should I update line 4? Right now, installation instructions do not mention anything about updating the file, or am I wrong? — Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAWEOMVBZKQOEAYOAHC3PBTX4E56PANCNFSM6AAAAAAYT4HWUI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[gcroci2]

Oh, sorry I didn't open the run_pdbprep.sh script so I had no clue that the above error was coming from not having defined the Pras path (it's not explicit about that). I would definitely update the installation instructions mentioning this.

Also, within the Pras_Server repo, what's the relative path for PRAS_exec file? @joaomcteixeira