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<div>Dear Minho Lee, </div>
<div><br>
</div>
<div>As you mentioned, we looked at the quota of 'swap' memory through the 'file' command.</div>
<div><br>
</div>
<div>The SWAP memory was allocated at 32 GB, but the actual memory was only 3 GB.</div>
<div><br>
</div>
<div>While checking the SCF's log file, I found something different from the previous one.</div>
<div><br>
</div>
<div>Processes (MPI) and Threads (openMP) used in the calculation are the same as 8 and 4 respectively,</div>
<div><br>
</div>
<div>Successful calculations before reinstalling the computer include the following:</div>
<div><br>
</div>
<div> Parallel version (MPI & OpenMP), running on 32 processor cores</div>
<div> Number of MPI processes: 8</div>
<div> Threads / MPI process: 4</div>
<div> R & G space division: proc / nbgrp / npool / nimage = 32</div>
<div> Reading input from espresso.in</div>
<div><br>
</div>
<div>However, in the current log file, there are four nodes separated as follows.</div>
<div><br>
</div>
<div> Parallel version (MPI & OpenMP), running on 4 processor cores</div>
<div> Number of MPI processes: 1</div>
<div> Threads / MPI process: 4</div>
<div><br>
</div>
<div> MPI processes distributed on 1 nodes</div>
<div><br>
</div>
<div>This seems to be the cause of exceeding the memory of my computer .. Do you know why this happens?</div>
<div><br>
</div>
<div>Thank you!</div>
<br>
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<p style="margin-top:0; margin-bottom:0">-------------------------------------</p>
<p style="margin-top:0; margin-bottom:0">Moon TaeHwan</p>
<p style="margin-top:0; margin-bottom:0">Chung-Ang University</p>
<p style="margin-top:0; margin-bottom:0">th4512@cau.ac.kr</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>보낸 사람:</b> Minho Lee <mino@simulation.re.kr> 대신 users <users-bounces@lists.quantum-espresso.org><br>
<b>보낸 날짜:</b> 2018년 9월 7일 금요일 오전 10:29:00<br>
<b>받는 사람:</b> Quantum Espresso users Forum<br>
<b>제목:</b> Re: [QE-users] (no subject)</font>
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<div name="x_messageBodySection" style="font-size:14px">Dear TaeHwan Moon,
<div><br>
</div>
<div>I’m sorry for the typo(ion_positions->atomic_positions )</div>
<div><br>
</div>
<div>Did you check your output?</div>
<div><br>
</div>
<div>In the standard output, you can find “estimated …..RAM ….” lines.</div>
<div><br>
</div>
<div>and you can check real memory usage of your computer via linux command “free”</div>
<div><br>
</div>
<div>If physical memory of your computer is not enough, “Swap” will be increased</div>
<div><br>
</div>
<div>Sincerly,</div>
</div>
<div name="x_messageSignatureSection" style="font-size:14px"><br>
Minho Lee<br>
------------------------<br>
Minho Lee<br>
CEO/Developer<br>
T. 02-3293-0204 | C. 010-2770-4080<br>
E. mino@virtuallab.co.kr | H. http://www.virtuallab.co.kr<br>
<br>
On-demand Materials Simulation<br>
https://www.materialssquare.com</div>
<div name="x_messageReplySection" style="font-size:14px">On 7 Sep 2018, 9:51 AM +0900, 문태환 <th4512@cau.ac.kr>, wrote:<br>
<blockquote type="cite" style="margin:5px 5px; padding-left:10px; border-left:thin solid #1abc9c">
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<div>Dear Minho Lee, </div>
<div><br>
</div>
<div>Thank you for your kind reply.</div>
<div><br>
</div>
<div>If you are talking about ATOMIC_POSITIONS, I thought I took a lot of text, so I excluded it when I wrote!</div>
<div><br>
</div>
<div>I have run the calculations by reducing the Processes (MPI) to 4, but the calculations are still going smoothly without exceeding the memory.</div>
<div><br>
</div>
<div>But my PC does not use CPU well and calculation speed is slow.</div>
<div><br>
</div>
<div>Like the Gaussian program,</div>
<div><br>
</div>
<div>Do you know how to control the memory while allocating a lot of CPU in the calculation?</div>
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<p style="margin-top:0; margin-bottom:0">-------------------------------------</p>
<p style="margin-top:0; margin-bottom:0">Moon TaeHwan</p>
<p style="margin-top:0; margin-bottom:0">Chung-Ang University</p>
<p style="margin-top:0; margin-bottom:0">th4512@cau.ac.kr</p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>보낸 사람:</b> Minho Lee <mino@simulation.re.kr> 대신 users <users-bounces@lists.quantum-espresso.org><br>
<b>보낸 날짜:</b> 2018년 9월 6일 목요일 오후 8:17:16<br>
<b>받는 사람:</b> users@lists.quantum-espresso.org; Quantum Espresso users Forum<br>
<b>제목:</b> Re: [QE-users] (no subject)</font>
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<div name="x_x_messageBodySection" style="font-size:14px">Dear Taehwan Moon,
<div><br>
</div>
<div>I can’t find the &ION namelist in your script,</div>
<div><br>
</div>
<div>I think you need to set ion_positions</div>
<div><br>
</div>
<div>Sincerely,</div>
</div>
<div name="x_x_messageSignatureSection" style="font-size:14px"><br>
Minho Lee<br>
------------------------<br>
Minho Lee<br>
CEO/Developer<br>
T. 02-3293-0204 | C. 010-2770-4080<br>
E. mino@virtuallab.co.kr | H. http://www.virtuallab.co.kr<br>
<br>
On-demand Materials Simulation<br>
https://www.materialssquare.com</div>
<div name="x_x_messageReplySection" style="font-size:14px">On 2018년 9월 6일 PM 7:48 +0900, 문태환 <th4512@cau.ac.kr>, wrote:<br>
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<div>Hello! Quantum espresso users.</div>
<div>I am a beginner user of QE and Linux, and I am having a lot of computation difficulties.</div>
<div>I need to calculate the SCF, DOS, and Band structure using a CIF file with zero-dimensional organic-inorganic hybrid materials.</div>
<div>However, when the SCF calculation starts and after an hour or so has elapsed, the memory problem causes an error.</div>
<div>My computer has 32 core CPU and 64GB of memory. <span>In the case of the CPU, there is room for using 8 cores when executing calculations.</span></div>
<div><span><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">(Processes (MPI) and Threads (openMP) use 8 and 4, respectively.)</span><br>
</span></div>
<div><span><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><br>
</span></span></div>
<div>The input file looks like this:</div>
<div><br>
</div>
<div>
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Can you give me advice to solve this problem?</div>
<div style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">
Please help me .. Thank you.</div>
<br>
</div>
<div><br>
</div>
<div>&CONTROL</div>
<div> calculation = "scf"</div>
<div> max_seconds = 8.64000e+04</div>
<div> pseudo_dir = "/home/user/.burai/.pseudopot"</div>
<div> restart_mode = "from_scratch"</div>
<div> tprnfor = .FALSE.</div>
<div> tstress = .FALSE.</div>
<div>/</div>
<div><br>
</div>
<div>&SYSTEM</div>
<div> a = 1.19962e+01</div>
<div> b = 1.46765e+01</div>
<div> c = 1.38899e+01</div>
<div> constrained_magnetization = "none"</div>
<div> cosac = -5.92053e-02</div>
<div> degauss = 1.00000e-02</div>
<div> ecutrho = 5.06000e+02</div>
<div> ecutwfc = 5.62066e+01</div>
<div> ibrav = -12</div>
<div> lda_plus_u = .FALSE.</div>
<div> nat = 192</div>
<div> nosym = .FALSE.</div>
<div> nspin = 1</div>
<div> ntyp = 5</div>
<div> occupations = "smearing"</div>
<div> smearing = "guassian"</div>
<div> starting_magnetization(1) = 0.00000e+00</div>
<div>/</div>
<div><br>
</div>
<div>&ELECTRONS</div>
<div> conv_thr = 1.00000e-06</div>
<div> diago_david_ndim = 4</div>
<div> diagonalization = "david"</div>
<div> electron_maxstep = 100</div>
<div> mixing_beta = 7.00000e-01</div>
<div> mixing_mode = "plain"</div>
<div> mixing_ndim = 8</div>
<div> startingpot = "atomic"</div>
<div> startingwfc = "atomic+random"</div>
<div>/</div>
<div><br>
</div>
<div>K_POINTS {automatic}</div>
<div> 3 3 3 0 0 0</div>
<div><br>
</div>
<div>ATOMIC_SPECIES</div>
<div>Bi 208.98038 Bi.pbe-dn-kjpaw_psl.1.0.0.UPF</div>
<div>Br 79.90400 Br.pbe-dn-kjpaw_psl.1.0.0.UPF</div>
<div>N 14.00674 N.pbe-n-kjpaw_psl.1.0.0.UPF</div>
<div>H 1.00794 H.pbe-kjpaw_psl.1.0.0.UPF</div>
<div>C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF</div>
<div><br>
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<p style="margin-top:0; margin-bottom:0">-------------------------------------</p>
<p style="margin-top:0; margin-bottom:0">Moon TaeHwan</p>
<p style="margin-top:0; margin-bottom:0">Chung-Ang University</p>
<p style="margin-top:0; margin-bottom:0">th4512@cau.ac.kr</p>
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